ABSTRACT
Although enhanced performances of photovoltaic devices by embedding metal nanoparticals in charge transport layer, doping into active layer bulk, decorating the active layer surface, and inserting at the interface between semiconductor and the electrode were reported, the effect of incorporating metal NPs at the interface of single crystal semiconductor and perovskite is rarely tackled. Herein the effects of incorporating Ag nanoparticals (AgNPs) at p-Si/MAPbI3 perovskite interface on the photodiode performances were investigated. The results showed that compared with reference device (without AgNPs) the photoresponsivity of the device incorporating AgNPs is greatly improved with the exception for light with wavelengths fall in the spectral range where AgNPs have strong optical absorption. This effect is extremely significant for relatively shorter wavelengths in visible region, and a maximal improvement of around 10.6 times in photoresponsivity was achieved. The physical origin of the exception for spectral range that AgNPs have strong optical absorption is the cancelation of scatter resulted enhancement through AgNPs by band-to-band absorption resulted reduction of photocurrent, in which the generated electron has energy near the fermi level and the hole has large effective mass, which relax by nonradiative recombination, thus making not contribution to the photocurrent. More importantly, the AgNP decorated device showed much faster photo response speed than reference device, and a maximal improvement of around 7.9 times in rise and fall time was achieved. These findings provide a novel approach for high responsive and high speed detection for weak light.
ABSTRACT
Camellia oleifera oil (CO oil) extracted from C. oleifera seeds has a 2300-year consumption history in China. However, there is relatively little research regarding its non-edible uses. This study determined the physicochemical properties of CO oil extracted via direct pressing, identified its main components using GC-MS, and evaluated its antioxidant, moisturizing, and anti-inflammatory activities. The results revealed that CO oil's acid, peroxide, iodine, and saponification values were 1.06 ± 0.031 mg/g, 0.24 ± 0.01 g/100 g, 65.14 ± 8.22 g/100 g, and 180.41 ± 5.60 mg/g, respectively. CO oil's tocopherol, polyphenol, and squalene contents were 82.21 ± 9.07 mg/kg, 181.37 ± 3.76 mg/kg, and 53.39 ± 6.58 mg/kg, respectively; its unsaturated fatty acid (UFA) content was 87.44%, and its saturated fatty acid (SFA) content was 12.56%. CO oil also demonstrated excellent moisture retention properties, anti-inflammatory effects, and certain free radical scavenging. A highly stable CO oil emulsion with competent microbiological detection was developed using formulation optimization. Using CO oil in the emulsion significantly improved the formulation's antioxidant and moisturizing properties compared with those of the emulsion formulation that did not include CO oil. The prepared emulsion was not cytotoxic to cells and could reduce cells' NO content; therefore, it may have potential nutritional value in medicine and cosmetics.
Subject(s)
Anti-Inflammatory Agents , Antioxidants , Camellia , Plant Oils , Camellia/chemistry , Antioxidants/pharmacology , Antioxidants/chemistry , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/chemistry , Plant Oils/pharmacology , Plant Oils/chemistry , Humans , Animals , Mice , Gas Chromatography-Mass SpectrometryABSTRACT
BACKGROUND: GATA transcription factors are type IV zinc-finger proteins that play key roles in plant growth and responses to environmental stimuli. Although these proteins have been studied in model plants, the related studies of GATA gene family under abiotic stresses are rarely reported in grapevine (Vitis vinifera L.). RESULTS: In the current study, a total of 23 VviGATA genes were identified in grapevine and classified into four groups (I, II, III, and IV), based on phylogenetic analysis. The proteins in the same group exhibited similar exon-intron structures and conserved motifs and were found to be unevenly distributed among the thirteen grapevine chromosomes. Accordingly, it is likely that segmental and tandem duplication events contributed to the expansion of the VviGATA gene family. Analysis of cis-acting regulatory elements in their promoters suggested that VviGATA genes respond to light and are influenced by multiple hormones and stresses. Organ/tissue expression profiles showed tissue specificity for most of the VviGATA genes, and five were preferentially upregulated in different fruit developmental stages, while others were strongly induced by drought, salt and cold stress treatments. Heterologously expressed VamGATA5a, VamGATA8b, VamGATA24a, VamGATA24c and VamGATA24d from cold-resistant V. amurensis 'Shuangyou' showed nuclear localization and transcriptional activity was shown for VamGATA5a, VamGATA8b and VamGATA24d. CONCLUSIONS: The results of this study provide useful information for GATA gene function analysis and aid in the understanding of stress responses in grapevine for future molecular breeding initiatives.
Subject(s)
GATA Transcription Factors , Vitis , GATA Transcription Factors/genetics , GATA Transcription Factors/metabolism , Vitis/metabolism , Phylogeny , Promoter Regions, Genetic/genetics , Stress, Physiological/genetics , Gene Expression Regulation, Plant , Plant Proteins/metabolism , Multigene FamilyABSTRACT
Employing a photosensitive donor/acceptor planar heterojunction (DA-PHJ) with complementary optical absorption as the active layer is one of the key strategies for realizing broad spectral organic photodiodes (BS-OPDs). To achieve superior optoelectronic performance, it is vital to optimize the thickness ratio of the donor layer to acceptor layer (the DA thickness ratio) in addition to the optoelectronic properties of the DA-PHJ materials. In this study, we realized a BS-OPD exploiting tin(II) phthalocyanine (SnPc)/3,4,9,10-perylenete-acarboxylic dianhydride (PTCDA) as the active layer and investigated the effect of the DA thickness ratio on the device performance. The results showed that the DA thickness ratio has a significant impact on the device performance, and an optimized DA thickness ratio of 30:20 was found. Upon the optimization of the DA thickness ratio, improvements of 187% in photoresponsivity and 144% in specific detectivity were achieved on average. Trap-free space-charge-limited photocarrier transport and balanced optical absorption over the wavelength range can be ascribed to the improved performance at the optimized DA thickness ratio. These results establish a solid photophysical foundation for improving the performance of BS-OPDs via thickness ratio optimization.
Subject(s)
Isoindoles , TinABSTRACT
The spread of disease on complex networks has attracted wide attention in physics, mathematics, and epidemiology. Recent works have demonstrated that individuals always exhibit different criteria for disease infection in a network that significantly influences the epidemic dynamics. In this paper, considering the heterogeneity of node susceptibility, we proposed an infection threshold model with neighbor resource support. The infection threshold of an individual is associated with the degree, and a parameter follows the normal distribution. Based on improved heterogeneous mean-field theory and extensive numerical simulations, we find that the mean and standard deviation of the infection threshold model can affect the phase transition and epidemic outbreak size. As the mean of the normal distribution parameter increases from a small value to a large value, the system shows a change from a continuous phase transition to a discontinuous phase transition, and the disease even stops spreading. The disease spreads from a discontinuous phase transition to continuous for the sizeable mean value as the standard deviation increases. Furthermore, the standard deviation also varies in the outbreak size.
Subject(s)
Epidemics , Disease Outbreaks , Humans , Normal Distribution , Physics , Social NetworkingABSTRACT
BACKGROUND: The characterization of colonization and dynamic changes related to gut microorganisms might be vital, as it presents an opportunity to quantify the co-variation between stocking densities and gut microbiome of dynamic distribution. The objective of this study was to determine the stocking density on physiological performance and dynamic distribution of gut microbiome (including bacterial and fungal communities) of Langya laying hens in the two development stages. METHODS: A randomized design with 2 × 3 factorial controls consisting of two development stages (24, 43 weeks-old) with three different stocking densities was performed. Three different stocking densities were allocated to a total of 300 11-week-old Langya laying hens (450 cm2/bird, 675 cm2/bird, 900 cm2/bird). Three housing densities were accomplished by raising different chickens per cage with the same floor size. The dependent variables of stocking densities at each sampling point were; growth performance, organs index, egg quality and the changes of dynamic gut bacterial and fungal communities in the cecum. RESULTS: Results showed that the stocking density didn't affect liver index, eggshell thickness, breaking shell strength and egg shape index. Hens from the highest stocking density had the lowest body weight, fallopian tube index, egg weight and yolk colour score. Except for the yolk colour score, the measurement changes caused by age followed the opposite pattern as stocking density. We observed a substantial rise in taxa linked with health threats when stocking density was increased, including Talaromyces, Oscillospiraceae_UCG-002, Oscillospira, and Dielma. The opposite was observed with Bacteroides, Bifidobacterium, Lachnoclostridium, Eisenbergiella, and Kurtzmaniella. Also, most taxa were linked to polymicrobial infection in clinical cases, especially species whose percentage declined as the hens aged, such as Terrisporobacter, Faecalicoccus, Dialister, Cylindrocarpon etc. Whereas Sellimonas, Mitsuokella, Eurotium, Wardomyces and Cephalotheca had the opposite trend. CONCLUSION: We speculated that excessive high density drove the abundance of bacteria and fungi connected with health problems. Where the gut microecology gradually reach a mature and balance status with age. Overall, this study demonstrates gut microbiome ecological processes in Langya layers at various stocking densities and finds possible connections between stocking density, microbiome and production performance. Our study will contribute to new insights associating suitable density patterns and production performance in laying hens by harnessing such a relative microbiome.
Subject(s)
Animal Husbandry/methods , Chickens/microbiology , Chickens/physiology , Gastrointestinal Microbiome , Mycobiome , Age Factors , Animals , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Female , Fungi/classification , Fungi/genetics , Fungi/isolation & purification , Housing, AnimalABSTRACT
BACKGROUND: In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. RESULTS: In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5' isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5' isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. CONCLUSIONS: Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression.
Subject(s)
Promoter Regions, Genetic/genetics , Protein Biosynthesis , Sequence Analysis , Transcription Initiation Site , Gene Expression Profiling , HEK293 Cells , Humans , RNA, Messenger/geneticsABSTRACT
Cooperative routing is one of the most widely used technologies for improving the energy efficiency and energy balance of wireless multi-hop networks. However, the end-to-end energy cost and network lifetime are greatly restricted if the cooperative transmission model is not designed properly. The main aim of this paper is to explore a two-stage cooperative routing scheme to further improve the energy efficiency and prolong the network lifetime. A two-stage cooperative (TSC) transmission model is firstly designed in which the core helper is introduced to determine the helper set for cooperation. Then, the two-stage link cost is formulated where x, the weight of residual energy, is introduced to be adjusted for different design goals. By selecting the optimal helper set, the two-stage link cost of each link can be optimized. Finally, based on the designed TSC transmission model and the optimized two-stage link cost, a distributed two-stage cooperative routing (TSCR) scheme is further proposed to minimize the end-to-end cooperative routing cost. Simulation results evaluate the effect of x on the different performance metrics. When x equals 0, TSCR can achieve the shortest end-to-end transmission delay and highest energy efficiency, while a larger x can achieve a longer network lifetime. Furthermore, simulation results also show that the proposed TSCR scheme can effectively improve both the energy efficiency and network lifetime compared with the existing schemes.
ABSTRACT
The major latex protein/ripening-related protein (MLP/RRP) subfamily is known to be involved in a wide range of biological processes of plant development and various stress responses. However, the biological function of MLP/RRP proteins is still far from being clear and identification of them may provide important clues for understanding their roles. Here, we report a genome-wide evolutionary characterization and gene expression analysis of the MLP family in European Vitis species. A total of 14 members, was found in the grape genome, all of which are located on chromosome 1, where are predominantly arranged in tandem clusters. We have noticed, most surprisingly, promoter-sharing by several non-identical but highly similar gene members to a greater extent than expected by chance. Synteny analysis between the grape and Arabidopsis thaliana genomes suggested that 3 grape MLP genes arose before the divergence of the two species. Phylogenetic analysis provided further insights into the evolutionary relationship between the genes, as well as their putative functions, and tissue-specific expression analysis suggested distinct biological roles for different members. Our expression data suggested a couple of candidate genes involved in abiotic stresses and phytohormone responses. The present work provides new insight into the evolution and regulation of Vitis MLP genes, which represent targets for future studies and inclusion in tolerance-related molecular breeding programs.
Subject(s)
Arabidopsis/genetics , Evolution, Molecular , Gene Expression Regulation, Plant , Genome, Plant , Plant Proteins/metabolism , Vitis/metabolism , Amino Acid Sequence , Chromosome Mapping , Gene Expression Profiling , Multigene Family , Phylogeny , Plant Proteins/genetics , Sequence Alignment , Synteny , Vitis/genetics , Vitis/growth & developmentABSTRACT
RATIONALE: It is of great significance to investigate the interaction of the metallodrug cisplatin (cis-[PtCl2 (NH3 )2 ]) with myoglobin for understanding of the mechanism of action of cisplatin and the overexpression of myoglobin in tumor cells. METHODS: The reactions of cisplatin and myoglobin were incubated under different conditions. A mass spectrometry (MS)-based strategy combining full proteolysis and limited proteolysis was developed for comprehensive studies of cisplatin-myoglobin interaction. RESULTS: The binding sites of cisplatin on myoglobin were identified as Trp14, His64, His81, His113 and His116 using electrospray ionization multiple-stage tandem mass spectrometry (ESI-MSn ) without liquid chromatography (LC) separation. The relative abundances of digested peptides from platinated myoglobin were obviously higher than those from native samples by limited proteolysis. CONCLUSIONS: An alternative and simple approach was developed to successfully monitor conformational changes of myoglobin induced by cisplatin binding using an ESI-MS-based quantification method combined with limited proteolysis. Meanwhile, His64 was firstly found to coordinate to platinum, which was likely to affect hydrogen bonds with the oxygen in the heme group. Copyright © 2016 John Wiley & Sons, Ltd.
Subject(s)
Binding Sites , Cisplatin/chemistry , Cisplatin/metabolism , Myoglobin/chemistry , Myoglobin/metabolism , Spectrometry, Mass, Electrospray Ionization/methods , Animals , Cisplatin/analysis , Horses , Muscle, Skeletal/chemistry , Myoglobin/analysis , Peptide Fragments/analysis , Peptide Fragments/chemistry , Peptide Fragments/metabolismABSTRACT
Cisplatin has been widely used in the chemotherapy of a variety of tumors, and the interactions of cisplatin with proteins play very important roles in its side effects and drug resistance, as well as its pharmacokinetics and the biodistribution. Insulin-like growth factor-1 (IGF-1) was found to be associated with the drug resistance of cisplatin. Here, the interaction between cisplatin and IGF-1 was investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. IGF-1-Pt(NH3)Cl was the main mono-adduct and the trans labilization was important to the reaction between IGF-1 and cisplatin, while another special mono-adduct IGF-1-Pt(NH3)Cl2 was observed. The rapid and sensitive top-down mass spectrometry-based approach in linear ion trap mass spectrometer has been developed to identify the binding sites of cisplatin in IGF-1 directly without tedious enzyme digestion. Three binding sites (Met59, Arg56 and Cys6) of cisplatin in IGF-1 were determined. The results not only provide a rapid and efficient way to identify the platinum binding sites in proteins, but also indicate that the binding of cisplatin could promote the fragmentation of IGF-1 and the rupture of disulfide bond.
Subject(s)
Antineoplastic Agents/chemistry , Cisplatin/chemistry , Insulin-Like Growth Factor I/chemistry , Amino Acid Sequence , Binding Sites , Fourier Analysis , Molecular Sequence Data , Protein Binding , Spectrometry, Mass, Electrospray IonizationABSTRACT
Vitis amurensis Rupr. is an exceptional wild-growing Vitis (grape) species that can safely survive a wide range of cold conditions, but the underlying cold-adaptive mechanism associated with gene regulation is poorly investigated. We have analyzed the physiochemical and transcriptomic changes caused by cold stress in a cold-tolerant accession, 'Heilongjiang seedling', of Chinese wild V. amurensis. We statistically determined that a total of 6,850 cold-regulated transcripts were involved in cold regulation, including 3,676 up-regulated and 3,174 down-regulated transcripts. A global survey of messenger RNA revealed that skipped exon is the most prevalent form of alternative spicing event. Importantly, we found that the total splicing events increased with the prolonged cold stress. We also identified thirty-eight major TF families that were involved in cold regulation, some of which were previously unknown. Moreover, a large number of candidate pathways for the metabolism or biosynthesis of secondary metabolites were found to be regulated by cold, which is of potential importance in coordinating cold tolerance with growth and development. Several heat shock proteins and heat shock factors were also detected to be intensively cold-regulated. Furthermore, we validated the expression profiles of 16 candidates using qRT-PCR to further confirm the accuracy of the RNA-seq data. Our results provide a genome-wide view of the dynamic changes in the transcriptome of V. amurensis, in which it is evident that various structural and regulatory genes are crucial for cold tolerance/adaptation. Moreover, our robust dataset advances our knowledge of the genes involved in the complex regulatory networks of cold stress and leads to a better understanding of cold tolerance mechanisms in this extremely cold-tolerant Vitis species.
Subject(s)
Adaptation, Physiological/genetics , Cold Temperature , Gene Expression Profiling , Gene Expression Regulation, Plant , Stress, Physiological/genetics , Vitis/genetics , Cell Nucleus/ultrastructure , Chloroplasts/ultrastructure , Cluster Analysis , Gene Ontology , Genes, Plant/genetics , Microscopy, Electron, Transmission , Oligonucleotide Array Sequence Analysis , Plant Leaves/genetics , Plant Leaves/ultrastructure , Plant Proteins/genetics , Reverse Transcriptase Polymerase Chain Reaction , Vitis/ultrastructureABSTRACT
Glycosylation is one of the most important posttranslational modifications of proteins and plays essential roles in various biological processes. Aberration in the glycan moieties of glycoproteins is associated with many diseases. It is especially critical to develop the rapid and sensitive methods for analysis of aberrant glycoproteins associated with diseases. Mass spectrometry (MS) has become a powerful tool for glycoprotein analysis. Especially, tandem mass spectrometry can provide highly informative fragments for structural identification of glycoproteins. This review provides an overview of the development of MS technologies and their applications in identification of abnormal glycoproteins and glycans in human serum to screen cancer biomarkers in recent years.
ABSTRACT
Basic helix-loop-helix (bHLH)-type transcription factors play diverse roles in plant physiological response and stress-adaptive regulation network. Here, we identified one grapevine bHLH transcription factor from a cold-tolerant accession 'Heilongjiang seedling' of Chinese wild Vitis amurensis (VabHLH1) as a transcriptional activator involved in cold stress. We also compared with its counterpart from a cold-sensitive Vitis vinifera cv. Cabernet Sauvignon (VvbHLH1). These two putative proteins are characterized by the presence of the identically conserved regions of 54 amino acid residues of bHLH signature domain, and shared 99.1% amino acid identity, whereas several stress-related cis-regulatory elements located in both promoter regions differed in types and positions. Expressions of two bHLHs in grapevine leaves were induced by cold stress, but evidently differ between two grapevine genotypes upon cold exposure. Two grapevine bHLH proteins were exclusively localized to the nucleus and exhibited strong transcriptional activation activities in yeast cells. Overexpression of either VabHLH1 or VvbHLH1 transcription factor did not affect the growth and development of transgenic Arabidopsis plants, but enhanced tolerance to cold stress. The improved tolerance in VabHLH1- or VvbHLH1-overexpressing Arabidopsis plants is associated with multiple physiological and biochemical changes that occurred during the time-course cold stress. These most common changes include the evaluated levels of proline, decreased amounts of malondialdehyde and reduced membrane injury as reflected by electrolyte leakage. VabHLH1 and VvbHLH1 displayed overlapping, but not identical, roles in activating the corresponding CBF cold signaling pathway, especially in regulating the expression of CBF3 and RD29A. Our findings demonstrated that two grapevine bHLHs act as positive regulators of the cold stress response, modulating the level of COR gene expression, which in turn confer tolerance to cold stress.
Subject(s)
Arabidopsis Proteins/physiology , Arabidopsis/physiology , Basic Helix-Loop-Helix Transcription Factors/physiology , Cold-Shock Response , Trans-Activators/physiology , Vitis/genetics , Amino Acid Sequence , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Basic Helix-Loop-Helix Transcription Factors/genetics , DNA, Plant/genetics , Gene Expression Regulation, Plant , Molecular Sequence Data , Plant Leaves/genetics , Plant Leaves/physiology , Plants, Genetically Modified/genetics , Plants, Genetically Modified/physiology , Plasmids , Trans-Activators/genetics , Transcription FactorsABSTRACT
Platinum drugs have become one of the most important kinds of chemotherapy agents, and the interactions of these drugs with proteins play very important roles in their side effects and drug resistance. However, it is still a challenge to determine the binding sites of platinum drugs in proteins with multiple disulfide bonds and stable three-dimensional structures using mass spectrometry. Here, the interaction between cisplatin and hen egg white lysozyme (HEWL), a multi-disulfide-bond-containing protein with a stable three-dimensional structure, was investigated using Fourier transform ion cyclotron resonance mass spectrometry. Typical disulfide bond reduction with dithiothreitol/tris(2-carboxyethyl)phosphine before trypsin digestion destroyed the binding of cisplatin to HEWL, and no platination sites were found. Efficient trypsin digestion methods for HEWL-cisplatin adducts were developed to avoid the loss of platinum binding to protein. At 55 °C, platinated HEWL was digested directly by trypsin in 6 h, and multiple platinated peptides were observed. In 60% acetonitrile, the digestion time of platinated HEWL was shortened to 2 h, and most of the platinated peptides were observed. In addition, the reduction of the disulfide bonds of HEWL greatly accelerated the reaction between HEWL and cisplatin, and the potential binding sites of cisplatin in reduced HEWL could be easily recognized. On the basis of the above-mentioned methods, multiple binding sites of cisplatin in HEWL were first identified by mass spectrometry.
Subject(s)
Antineoplastic Agents/chemistry , Cisplatin/chemistry , Muramidase/chemistry , Amino Acid Sequence , Animals , Binding Sites , Chickens , Disulfides/chemistry , Fourier Analysis , Ions , Molecular Sequence Data , Peptides/chemistry , Solvents/chemistry , Spectrometry, Mass, Electrospray Ionization , Spectroscopy, Fourier Transform Infrared , Temperature , Trypsin/chemistryABSTRACT
To address the technical limitations of automatic coal and gangue detection technology in fully mechanized top coal caving mining operations, the low radiation level radioactivity measurement method is utilized to assess the degree of coal-gangue mixture in top coal caving process. This approach is based on the distinguishing radiation characteristics of natural γ-rays between coal and gangue. This study analyzed the distribution characteristics of natural γ-rays in coal and rock layers of thick coal seams and the applicability of this method, introduced the basic principle of coal-gangue detection technology based on natural γ-ray, developed the test system about automatic coal-gangue detection, studied the radiation characteristics of coal and gangue, proposed determination model of the coal-gangue mixed degree, combined with the time sequence characteristics of the top coal's releasing flow and the energy spectrum characteristics of different layers of rock, realized the precise coal-gangue detection technology in complex structure thick coal seam with multiple gangue. Field tests were conducted in Lilou, Xiaoyu and Tashan Coal Mine. The test results were well corroborated with the research results and achieved the expected results, which laid the foundation for the field application of intelligent coal mining.
ABSTRACT
Background: Prostate adenocarcinoma is a frequent cancer among men with high incidence and mortality rates. Biomarkers are useful for the treatment of cancers, so we need to explore the regulatory network of prostate adenocarcinoma. Method: The database from University of California Santa Cruz was used to determine expression of messenger RNAs and microRNAs. Weighted correlation network analysis was used for classifying genes. Search Tool for Recurring Instances of Neighboring Genes and Cytoscape were used for the construction of PPI network and selection of hub genes. The microRNAs were predicted in miRactDB. The relations between microRNAs and messenger RNAs were assessed by Statistical Product and Service Solutions. The prognostic value was evaluated through Kaplan-Meier method. Kyoto Encyclopedia of Genes and Genomes, Gene Ontology and Gene Set Enrichment Analysis were used for predicting potential function. Results: 10 hub genes were all overexpressed in tumor tissues compared to normal tissues, but only aurora kinase B and nucleolar and spindle associated protein 1 were both significantly related to disease-free interval and progression-free interval time.Aurora kinase B and nucleolar and spindle associated protein 1 were negatively related to hsa-miR-1-3p, hsa-miR-133a-3p, hsa-miR-133b and hsa-miR-221-3p but positively related to hsa-miR-15b-5p, hsa-miR-21-5p, hsa-miR-106b-5p, hsa-miR-183-5p, hsa-miR-191-5p, hsa-miR-210-3p, hsa-miR-425-5p and hsa-miR-653-5p. All microRNAs except has-miR-653-5p significantly were related to the disease-free interval and progression-free interval time. The functions of microRNAs were enriched in cell cycle. Conclusion: We identified hub messenger RNAs and core microRNAs and established a novel messenger RNA-microRNA network associated with the prognosis of prostate adenocarcinoma.
ABSTRACT
In many perennial fruit species, including grapevine (Vitis vinifera L.), the highly complex process of somatic embryogenesis (SE) can result in the formation of a deformed embryo, although the underlying reasons are still poorly understood. Here, V. vinifera cv. 'Chardonnay' cotyledonary embryos with distinct morphologies were used to address this issue. Normal cotyledonary embryos (NCEs) and elongated cotyledonary embryos (ECEs) were observed to have better-developed vasculature and shoot meristems than the vitrified cotyledonary embryos (VCEs) and fused cotyledonary embryos (FCEs), but ECEs were less developed. We determined that the morphological differences in these phenotypically abnormal embryos were likely associated with endogenous hormone levels, since concentrations of the phytohormones indoleacetic acid (IAA) and abscisic acid (ABA) in NCEs were higher than in the other three types. Comparative transcriptome analysis revealed large differences in gene expression of the hormone signaling pathways in normal and abnormal cotyledonary embryos. Weighted gene co-expression network analysis of the different cotyledonary types allowed the identification of co-regulated gene modules associated with SE, suggesting a role for ERF family genes and other transcription factors (TFs) in regulating morphology. Moreover, an analysis of morphology-specific gene expression indicated that the activation of a specific protein kinase, small heat shock proteins (sHSPs) and certain TFs was closely associated with the formation of normal cotyledonary embryos. Our comparative analyses provide insights into the gene networks regulating somatic cotyledon development and open new avenues for research into plant regeneration and functional genomic studies of malformed embryos.
Subject(s)
Cotyledon , Vitis , Cotyledon/metabolism , Transcriptome , Vitis/physiology , Plant Growth Regulators , Hormones/metabolism , Gene Expression Regulation, Plant , Plant Proteins/genetics , Plant Proteins/metabolismABSTRACT
In globally cultivated grapevines, low-temperature stress poses a persistent challenge. Although COLD1 is recognized as a cold receptor in rice, its function in grapevine cold signaling is unclear. Here, we identified VaCOLD1, a transmembrane protein from the cold-tolerant Vitis amurensis Rupr, which is primarily located on plasma and endoplasmic reticulum membranes. Broadly expressed across multiple tissues, VaCOLD1 responds to various environmental stresses, particularly to cold. Its promoter contains distinct hormone- and stress-responsive elements, with GUS assays confirming widespread expression in Arabidopsis thaliana. Validation of interaction between VaCOLD1 and VaGPA1, together with their combined expression in yeast and grape calli, notably improved cold endurance. Overexpression of VaCOLD1 enhances cold tolerance in Arabidopsis by strengthening the CBF-COR signaling pathway. This is achieved through shielding against osmotic disturbances and modifying the expression of ABA-mediated genes. These findings emphasize the critical role of the VaCOLD1-VaGPA1 complex in mediating the response to cold stress via the CBF-COR pathway.
Subject(s)
Arabidopsis , Cold-Shock Response , Transcription Factors/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Arabidopsis/metabolism , Cold Temperature , Gene Expression Regulation, Plant , Plants, Genetically Modified/genetics , Plants, Genetically Modified/metabolismABSTRACT
Melatonin (MEL) is an antioxidant molecule that enhances plant tolerance to environmental stress. However, the mechanisms by which MEL regulates cold signaling pathways in grapes under cold stress remain elusive. Here, we investigated the physiological and transcriptomic changes in grape seedlings treated with exogenous MEL to determine their protective role under cold stress. Results showed that 150 µM MEL effectively attenuated cold-induced cell damage by reducing reactive oxygen species (ROS) and preserving the chloroplast structure and function. MEL also inhibited tannin degradation, which contributed to its protective effect. Exogenous MEL promoted the synthesis of endogenous MEL, abscisic acid, auxin, and cytokinin while inhibiting gibberellin. Transcriptomic profiling revealed 776 differentially expressed transcripts in MEL-treated samples compared to controls. Functional analysis of a candidate hub gene, VvHSFA6b, showed that its overexpression in grape calli enhances cold tolerance by activating jasmonic acid synthesis pathway genes, promoting JA accumulation, and inhibiting JAZ-repressed transcription factors.