3D Gaussian Splatting as New Era: A Survey.

3D Gaussian Splatting (3D-GS) has emerged as a significant advancement in the field of Computer Graphics, offering explicit scene representation and novel view synthesis without the reliance on neural networks, such as Neural Radiance Fields (NeRF). This technique has found diverse applications in areas such as robotics, urban mapping, autonomous navigation, and virtual reality/augmented reality, just name a few. Given the growing popularity and expanding research in 3D Gaussian Splatting, this paper presents a comprehensive survey of relevant papers from the past year. We organize the survey into taxonomies based on characteristics and applications, providing an introduction to the theoretical underpinnings of 3D Gaussian Splatting. Our goal through this survey is to acquaint new researchers with 3D Gaussian Splatting, serve as a valuable reference for seminal works in the field, and inspire future research directions, as discussed in our concluding section.

Strigolactones Might Regulate Ovule Development after Fertilization in Xanthoceras sorbifolium.

Strigolactones (SLs) were recently defined as a novel class of plant hormones that act as key regulators of diverse developmental processes and environmental responses. Much research has focused on SL biosynthesis and signaling in roots and shoots, but little is known about whether SLs are produced in early developing seeds and about their roles in ovule development after fertilization. This study revealed that the fertilized ovules and early developing pericarp in Xanthoceras sorbifolium produced minute amounts of two strigolactones: 5-deoxystrigol and strigol. Their content decreased in the plants with the addition of exogenous phosphate (Pi) compared to those without the Pi treatment. The exogenous application of an SL analog (GR24) and a specific inhibitor of SL biosynthesis (TIS108) affected early seed development and fruit set. In the Xanthoceras genome, we identified 69 potential homologs of genes involved in SL biological synthesis and signaling. Using RNA-seq to characterize the expression of these genes in the fertilized ovules, 37 genes were found to express differently in the fertilized ovules that were aborting compared to the normally developing ovules. A transcriptome analysis also revealed that in normally developing ovules after fertilization, 12 potential invertase genes were actively expressed. Hexoses (glucose and fructose) accumulated at high concentrations in normally developing ovules during syncytial endosperm development. In contrast, a low ratio of hexose and sucrose levels was detected in aborting ovules with a high strigolactone content. XsD14 virus-induced gene silencing (VIGS) increased the hexose content in fertilized ovules and induced the proliferation of endosperm free nuclei, thereby promoting early seed development and fruit set. We propose that the crosstalk between sugar and strigolactone signals may be an important part of a system that accurately regulates the abortion of ovules after fertilization. This study is useful for understanding the mechanisms underlying ovule abortion, which will serve as a guide for genetic or chemical approaches to promote seed yield in Xanthoceras.

Stachydrine represses the proliferation and enhances cell cycle arrest and apoptosis of breast cancer cells via PLA2G2A/DCN axis.

Considering the therapeutic efficacy of Stachydrine on breast cancer (BC), this study aims to decipher the relevant mechanism. The effects of Stachydrine on BC cell viability, proliferation and apoptosis were firstly investigated. Then, Bioinformatics was applied to sort out the candidate interacting with Stachydrine as well as its expression and downstream target in BC. Relative expressions of genes of interest as well as proliferation- and apoptosis-related factors in BC cells were quantified through quantitative reverse-transcription PCR and western blot as appropriate. As a result, Stachydrine inhibited the proliferation, down-regulated the expressions of proliferating cell nuclear antigen and CyclinD1, enhanced cell cycle arrest and apoptosis, and up-regulated the levels of Cleaved caspase-3 and Cleaved caspase-9 in BC cells. Phospholipase A2 Group IIA (PLA2G2A) was predicted as the candidate interacting with Stachydrine and to be lowly expressed in BC. PLA2G2A silencing reversed while PLA2G2A overexpression reinforced the effects of Stachydrine. Decorin (DCN) was the downstream target of PLA2G2A and also lowly expressed in BC. PLA2G2A silencing counteracted yet overexpressed PLA2G2A strengthened the promoting effects of Stachydrine on DCN level. Collectively, Stachydrine inhibits the growth of BC cells to promote cell cycle arrest and apoptosis via PLA2G2A/DCN axis.

Comparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus.

Yellow-seed trait is a desirable breeding characteristic of rapeseed (Brassica napus) that could greatly improve seed oil yield and quality. However, the underlying mechanisms controlling this phenotype in B. napus plants are difficult to discern because of their complexity. Here, we assemble high-quality genomes of yellow-seeded (GH06) and black-seeded (ZY821). Combining in-depth fine mapping of a quantitative trait locus (QTL) for seed color with other omics data reveal BnA09MYB47a, encoding an R2R3-MYB-type transcription factor, as the causal gene of a major QTL controlling the yellow-seed trait. Functional studies show that sequence variation of BnA09MYB47a underlies the functional divergence between the yellow- and black-seeded B. napus. The black-seed allele BnA09MYB47aZY821, but not the yellow-seed allele BnA09MYB47aGH06, promotes flavonoid biosynthesis by directly activating the expression of BnTT18. Our discovery suggests a possible approach to breeding B. napus for improved commercial value and facilitates flavonoid biosynthesis studies in Brassica crops.

Combining transcriptomics and metabolomics to identify key response genes for aluminum toxicity in the root system of Brassica napus L. seedlings.

KEY MESSAGE: By integrating QTL mapping, transcriptomics and metabolomics, 138 hub genes were identified in rapeseed root response to aluminum stress and mainly involved in metabolism of lipids, carbohydrates and secondary metabolites. Aluminum (Al) toxicity has become one of the important abiotic stress factors in areas with acid soil, which hinders the absorption of water and nutrients by roots, and consequently retards the growth of crops. A deeper understanding of the stress-response mechanism of Brassica napus may allow us to identify the tolerance gene(s) and use this information in breeding-resistant crop varieties. In this study, a population of 138 recombinant inbred lines (RILs) was subjected to aluminum stress, and QTL (quantitative trait locus) mapping was used to preliminarily locate quantitative trait loci related to aluminum stress. Root tissues from seedlings of an aluminum-resistant (R) line and an aluminum-sensitive (S) line from the RIL population were harvested for transcriptome sequencing and metabolome determination. By combining the data on quantitative trait genes (QTGs), differentially expressed genes (DEGs), and differentially accumulated metabolites (DAMs), key candidate genes related to aluminum tolerance in rapeseed were determined. The results showed that there were 3186 QTGs in the RIL population, 14,232 DEGs and 457 DAMs in the comparison between R and S lines. Lastly, 138 hub genes were selected to have a strong positive or negative correlation with 30 important metabolites (|R|≥ 0.95). These genes were mainly involved in the metabolism of lipids, carbohydrates and secondary metabolites in response to Al toxicity stress. In summary, this study provides an effective method for screening key genes by combining QTLs, transcriptome sequencing and metabolomic analysis, but also lists key genes for exploring the molecular mechanism of Al tolerance in rapeseed seedling roots.

Application of a Dual-Probe Coloading Nanodetection System in the Process Monitoring and Efficacy Assessment of Photodynamic Therapy: An In Vitro Study.

The oxygen-consuming property of photodynamic therapy (PDT) affects its effects and aggravates tumor hypoxia, thus upregulating the vascular endothelial growth factor (VEGF) to exacerbate tumor metastasis and lead to treatment failure. Therefore, it is necessary to monitor the dynamic changes in the factors related to PDT and tumor development trends in real time, thus helping to improve PDT efficiency. This study fabricated a fluorescent probe, TPE-2HPro, and a fluorescein-labeled aptamer probe, FAM-AptamerVEGF, to detect hydrogen peroxide (H2O2) and VEGF through the photoinduced electron-transfer effect and the specific affinity of the aptamer to VEGF, respectively. The two probes were loaded into the inner pores and absorbed on the surface of polydopamine coating-wrapped mesoporous silica nanoparticles (MSN@PDA) to construct the dual-probe-loaded system, MSNTH@PDAApt, which was kept stable in fetal bovine serum (FBS) solution and achieved pH-responsive release behavior, thus helping to increase the accumulation of the two probes in tumor cells. The dichloroacetic acid-mediated in vitro antitumor tests showed that the changing trends of H2O2 and VEGF levels were consistent with the results of related mechanism studies and could be monitored by MSNTH@PDAApt. The in vitro chlorin e6 (Ce6)-mediated PDT treatment demonstrated that when the illumination condition was 650 nm, 50 mW/cm2 for 10 min, cells were more inclined to metastasis and invasion rather than death due to a substantial increase in VEGF expression at the low Ce6 concentrations. With the increase of the Ce6 concentration, the growth of the H2O2 level gradually exceeded that of VEGF, and the reactive oxygen species (ROS)-mediated cell death dominated when the Ce6 concentration was about 2 times its IC50 values. Besides, hypoxia also affected the H2O2 and VEGF changes. These results demonstrated that MSNTH@PDAApt could precisely monitor and assess the tumor development trends during PDT treatment, thus helping improve the treatment effect.

Genetic mapping and physiological analysis of chlorophyll-deficient mutant in Brassica napus L.

BACKGROUND: Leaf color mutants have reduced photosynthetic efficiency, which has severely negative impacts on crop growth and economic product yield. There are different chlorophyll mutants in Arabidopsis and crops that can be used for genetic control and molecular mechanism studies of chlorophyll biosynthesis, chloroplast development and photoefficiency. Chlorophyll mutants in Brassica napus are mostly used for mapping and location research but are rarely used for physiological research. The chlorophyll-deficient mutant in this experiment were both genetically mapped and physiologically analyzed. RESULTS: In this study, yellow leaf mutant of Brassica napus L. mutated by ethyl methyl sulfone (EMS) had significantly lower chlorophyll a, b and carotenoid contents than the wild type, and the net photosynthetic efficiency, stomatal conductance and transpiration rate were all significantly reduced. The mutant had sparse chloroplast distribution and weak autofluorescence. The granule stacks were reduced, and the shape was extremely irregular, with more broken stromal lamella. Transcriptome data analysis enriched the differentially expressed genes mainly in phenylpropane and sugar metabolism. The mutant was mapped to a 2.72 Mb region on A01 by using BSA-Seq, and the region was validated by SSR markers. CONCLUSIONS: The mutant chlorophyll content and photosynthetic efficiency were significantly reduced compared with those of the wild type. Abnormal chloroplasts and thylakoids less connected to the stroma lamella appeared in the mutant. This work on the mutant will facilitate the process of cloning the BnaA01.cd gene and provide more genetic and physiological information concerning chloroplast development in Brassica napus.

Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance.

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

Research and Implementation of Mobile Internet Management Optimization and Intelligent Information System Based on Smart Decision.

The way by which artificial intelligence is implemented is similar to the thinking process of the human brain. People obtain information about external conditions through five senses, namely, vision, hearing, smell, taste, and touch, and, through the further processing of the brain, it forms meaningful decision-making elements. Then, through the process of analysis and reasoning, further decisions are made. In the information age, the application of intelligent management information systems in various fields has promoted the modernization and intelligence of social development. From the perspective of intelligent decision-making, this paper analyzes the requirements of intelligent information systems and designs an intelligent information system based on mobile Internet management optimization, including system management optimization, and proposes an environment-based layer, network transport layer, and the three-tier system architecture of the smart service application layer. Finally, this paper considers the problem of data fusion after system expansion. According to the existing fuzzy fusion algorithm, a weight-based fuzzy fusion algorithm is proposed. The simulation analysis shows that the algorithm can be effectively applied in intelligent information systems.

Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination.

BACKGROUND: Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting of the herbicide spray might affect the germination and growth of rapeseed, Brassica napus, so it is imperative to understand the response mechanism of rape to TBM during germination. The aim of this study was to use transcriptome analysis to reveal the gene responses in herbicide-tolerant rapeseed to TBM stress during seed germination. RESULTS: 2414, 2286, and 1068 differentially expressed genes (DEGs) were identified in TBM-treated resistant vs sensitive lines, treated vs. control sensitive lines, treated vs. control resistant lines, respectively. GO analysis showed that most DEGs were annotated to the oxidation-reduction pathways and catalytic activity. KEGG enrichment was mainly involved in plant-pathogen interactions, α-linolenic acid metabolism, glucosinolate biosynthesis, and phenylpropanoid biosynthesis. Based on GO and KEGG enrichment, a total of 137 target genes were identified, including genes involved in biotransferase activity, response to antioxidant stress and lipid metabolism. Biotransferase genes, CYP450, ABC and GST, detoxify herbicide molecules through physical or biochemical processes. Antioxidant genes, RBOH, WRKY, CDPK, MAPK, CAT, and POD regulate plant tolerance by transmitting ROS signals and triggering antioxidant enzyme expression. Lipid-related genes and hormone-related genes were also found, such as LOX3, ADH1, JAZ6, BIN2 and ERF, and they also played an important role in herbicide resistance. CONCLUSIONS: This study provides insights for selecting TBM-tolerant rapeseed germplasm and exploring the molecular mechanism of TBM tolerance during germination.

Role of ethylene in the regulatory mechanism underlying the abortion of ovules after fertilization in Xanthoceras sorbifolium.

KEY MESSAGE: Genes related to the MAPK cascade, ethylene signaling pathway, Pi starvation response, and NAC TFs were differentially expressed between normal and abortive ovules. Receptor-mediated ethylene signal perception and transmission play an important role in regulating fruit and ovule development. Xanthoceras sorbifolium, a small to medium-sized tree endemic to northern China, is an emerging dedicated oilseed crop designed for applications in advanced biofuel, engine oil, and functional food, as well as for pharmaceutical and cosmetic applications. Despite the importance of Xanthoceras seed oil, low seed productivity has constricted commercial exploitation of the species. The abortion of developing seeds (ovules after fertilization) is a major factor limiting fruit and seed production in the plant. To increase fruit and seed yields, a better understanding of the mechanisms underlying the abortion of fertilized ovules is critical. This study revealed differences in nucellus degeneration, endosperm development, and starch grain content between normally and abnormally developing ovules after fertilization. We constructed 6 RNA-sequencing (RNA-seq) libraries from normally and abnormally developing ovules at the onset of their abortion process. Comparative transcriptome analysis between the normal and abnormal ovules identified 818 differentially expressed genes (DEGs). Among DEGs, many genes involved in mitogen-activated protein kinase (MAPK) cascades, ethylene signaling pathway, and NAC transcription factor genes showed up-regulated expression in abnormal ovules. The RNA-seq data were validated using quantitative reverse-transcription PCR. Using virus-induced gene silencing (VIGS) methods, evaluation of an ethylene receptor gene (XsERS) function indicated that the gene was closely related to early development of fruits and seeds. Based on the data presented here, we propose a model for a MAPK-ethylene signaling-NAC2 gene regulatory cascade that plays an important role in the regulation of the ovule abortion process in X. sorbifolium. The present study is imperative for understanding the mechanisms of ovule abortion after fertilization and identifying the critical genes and gene networks involved in determining the fate of ovule development.

WIT120 data mining technology based on internet of things.

In recent years, with the increasing aging of society, the number of patients with chronic heart disease, hypertension and diabetes has increased dramatically. It has guiding significance for the prevention and treatment by long-term monitoring of the physiological signs of patients with chronic diseases, scoring statistical data, and predicting the development trend of users' health. The work used the data collected by WIT120 system to analyze the pre-processed thick data based on adaptive k-means clustering method under the MapReduce framework, and the GM (1,1) grey model was used to predict the future health status of users. The simulation results have verified the effectiveness of the proposed algorithm.

Photosynthetic index and nitrogen assimilation in rapeseed seedlings transplanted in soil with ammonium glufosinate / Índice fotossintético e assimilação de nitrogênio em plântulas de colza transplantadas em resposta a resíduos de glufosinato presentes no solo

ABSTRACT: Herbicide application is an effective weed control method for mitigating crop yield loss; however, herbicide overuse can cause toxicity in non-target plants. The present study evaluated the effects of glufosinate at recommended dose for agricultural application (0.45 kg ha-1) and at overuse dose (0.90 kg ha-1) glufosinate application on photosynthetic performance and nitrogen assimilation of the rapeseed varieties D148 and Zhongshuang 11 (ZS11). Both glufosinate concentrations significantly decreased the content of chlorophyll and nitrogenous compounds, except free proline, and the activity of glutamine synthetase and glutamate synthase, and increased the activity of glutamic acid dehydrogenase in both varieties. When the concentration of glyphosate was 0.45kg ha-1, the nitrogen assimilation of the two varieties decreased, which indicated that the recommended dosage inhibited the nitrogen assimilation of the two varieties; however, the increase of net photosynthetic rate of D148 and the decrease of that of ZS11 mean that D148 is more tolerant to the recommended dose of glyphosate than ZS11. The 0.90 kg ha-1 dosage was toxic to both rapeseed varieties. Overall, our results indicated that herbicide overuse inhibited the photosynthetic rate and nitrogen assimilation in rapeseed seedlings, and it is essential to apply a suitable glufosinate dose based on the variety grown to minimize adverse effects on crops and environment.

RESUMO: A aplicação de herbicidas é um método eficaz de controle de ervas daninhas para mitigar a perda de produtividade das culturas. No entanto, o uso excessivo de herbicidas pode causar toxicidade em plantas não alvo. O presente estudo avaliou os efeitos da dose recomendada para aplicação agrícola (0.45 kg ha-1) e dose excessiva (0.90 kg ha-1) de glufosinato no desempenho fotossintético e assimilação de nitrogênio das variedades de colza D148 e Zhongshuang 11 (ZS11). Ambas as concentrações de glutamato diminuíram significativamente o teor de clorofila e compostos azotados, exceto a prolina livre, e a atividade de síntese da glutamina e de síntese de glutamato, e aumentaram a atividade de desidrogenase do ácido glutâmico em ambas as variedades. Quando a concentração de glifosato foi 0.45 kg ha-1, a assimilação de azoto das duas variedades diminuiu, o que indicou que a dosagem recomendada de glifosato inibiu a assimilação de azoto das duas variedades de colza. Entretanto, a taxa fotosintética líquida do D148 aumentou enquanto o do ZS11 diminuiu, o que significa que o D148 é mais tolerante a dose recomendada de glifosato do que o ZS11. A dose de 0.90 kg ha-1 de glifosato foi prejudicial para as mudas de duas variedades de colza. Em geral, os nossos resultados indicam que o uso excessivo de glufosinato inibe a taxa fotossintética e a assimilação de nitrogênio em mudas de colza, sendo essencial aplicar uma dose adequada deste herbicida com base na variedade cultivada para minimizar os efeitos adversos nas culturas e no meio ambiente.

Inflammatory Cytokines and T-Lymphocyte Subsets in Serum and Sputum in Patients with Bronchial Asthma and Chronic Obstructive Pulmonary Disease.

BACKGROUND It can be difficult to distinguish between bronchial asthma and chronic obstructive pulmonary disease (COPD) clinically, although these conditions are associated with different profiles of inflammatory cytokines and immune cells. This study aimed to compare T-lymphocyte subsets and inflammatory cytokines in the serum and sputum of patients with bronchial asthma and COPD who had respiratory function testing. MATERIAL AND METHODS The study included 42 patients with bronchial asthma, 48 patients with COPD, and 45 patients with bronchial asthma complicated with COPD. The percentage predicted values of the forced expiratory volume in one second (FEV1), the forced vital capacity (FVC), and the peak expiratory flow (PEF) rate were measured. Serum and sputum levels of interleukin (IL)-4, IL-5, IL-9, IL-13, IL-1ß, IL-6 and tumor necrosis factor-alpha (TNF-alpha) were measured using an enzyme-linked immunosorbent assay (ELISA). Flow cytometry measured the CD4 and CD8 T-lymphocyte subsets, and the CD4: CD8 ratio was calculated. RESULTS The FEV1, FVC, and PEF were significantly lower in patients with COPD compared with the other two patient groups. Serum and sputum levels of IL-4, IL-5, IL-9 and IL-13 were significantly increased in the COPD patient group, and levels of TNF-alpha, IL-1ß and IL-6 were significantly increased in the bronchial asthma patient group. The CD4: CD8 ratio in sputum was lowest in bronchial asthma patient group and highest in COPD patient group. CONCLUSIONS The detection of serum and sputum inflammatory cytokines and T-lymphocyte subsets may distinguish between bronchial asthma and COPD.

The superoxide dismutase genes might be required for appropriate development of the ovule after fertilization in Xanthoceras sorbifolium.

KEY MESSAGE: Superoxide dismutase genes were expressed differentially along with developmental stages of fertilized ovules in Xanthoceras sorbifolium, and the XsMSD gene silencing resulted in the arrest of fertilized ovule development. A very small percentage of mature fruits (ca. 5%) are produced relative to the number of bisexual flowers in Xanthoceras sorbifolium because seeds and fruits are aborted at early stages of development after pollination. Reactive oxygen species (ROS) in plants are implicated in an extensive range of biological processes, such as programmed cell death and senescence. Superoxide dismutase (SOD) activity might be required to regulate ROS homeostasis in the fertilized ovules of X. sorbifolium. The present study identified five SOD genes and one SOD copper chaperone gene in the tree. Their transcripts were differentially expressed along different stages of fertilized ovule development. These genes showed maximum expression in the ovules at 3 days after pollination (DAP), a time point in which free nuclear endosperm and nucleus tissues rapidly develop. The XsCSD1, XsFSD1 and XsMSD contained seven, eight, and five introns, respectively. Analysis of the 5'-flanking region of XsFSD1 and XsMSD revealed many cis-acting regulatory elements. Evaluation of XsMSD gene function based on virus-induced gene silencing (VIGS) indicated that the gene was closely related to early development of the fertilized ovules and fruits. This study suggested that SOD genes might be closely associated with the fate of ovule development (aborted or viable) after fertilization in X. sorbifolium.

Comparative De Novo Transcriptome Analysis of Fertilized Ovules in Xanthoceras sorbifolium Uncovered a Pool of Genes Expressed Specifically or Preferentially in the Selfed Ovule That Are Potentially Involved in Late-Acting Self-Incompatibility.

Xanthoceras sorbifolium, a tree species endemic to northern China, has high oil content in its seeds and is recognized as an important biodiesel crop. The plant is characterized by late-acting self-incompatibility (LSI). LSI was found to occur in many angiosperm species and plays an important role in reducing inbreeding and its harmful effects, as do gametophytic self-incompatibility (GSI) and sporophytic self-incompatibility (SSI). Molecular mechanisms of conventional GSI and SSI have been well characterized in several families, but no effort has been made to identify the genes involved in the LSI process. The present studies indicated that there were no significant differences in structural and histological features between the self- and cross-pollinated ovules during the early stages of ovule development until 5 days after pollination (DAP). This suggests that 5 DAP is likely to be a turning point for the development of the selfed ovules. Comparative de novo transcriptome analysis of the selfed and crossed ovules at 5 DAP identified 274 genes expressed specifically or preferentially in the selfed ovules. These genes contained a significant proportion of genes predicted to function in the biosynthesis of secondary metabolites, consistent with our histological observations in the fertilized ovules. The genes encoding signal transduction-related components, such as protein kinases and protein phosphatases, are overrepresented in the selfed ovules. X. sorbifolium selfed ovules also specifically or preferentially express many unique transcription factor (TF) genes that could potentially be involved in the novel mechanisms of LSI. We also identified 42 genes significantly up-regulated in the crossed ovules compared to the selfed ovules. The expression of all 16 genes selected from the RNA-seq data was validated using PCR in the selfed and crossed ovules. This study represents the first genome-wide identification of genes expressed in the fertilized ovules of an LSI species. The availability of a pool of specifically or preferentially expressed genes from selfed ovules for X. sorbifolium will be a valuable resource for future genetic analyses of candidate genes involved in the LSI response.

A sensitive method for digoxin determination using formate-adduct ion based on the effect of ionization enhancement in liquid chromatograph-mass spectrometer.

A sensitive and rapid method based on formate-adduct ion detection was developed and fully validated for digoxin determination in rat plasma. For LC/MS/MS detection with formate-adducts as precursor ions, transitions of m/z 825.5→779.9 for digoxin and m/z 809.5→763.4 for the internal standard (digitoxin) were monitored in negative mode. To investigate the impact of formic acid on the mass response and method sensitivity, a formic acid concentration range of 0-0.1% (0, 0.0005%, 0.002%, 0.01%, 0.1%, v/v) was evaluated. A concentration of 0.002% gave the highest sensitivity, which was 16- to 18-fold higher than deprotonated ions, and was designated as the contribution giving the strongest ionization enhancement and adduction. A number of parameters were then varied in order to optimize the method, and a limit of quantitation (LOQ) at 0.2 ng/mL was reached with an injection volume of 5 µL, a total run time of 3 min, and 0.1 mL of rat plasma. A calibration curve was plotted over the range 0.2-50 ng/mL (R(2)=0.9998), and the method was successfully applied to study pharmacokinetics in rat following a single oral administration of digoxin (0.05 mg/kg). Four additional steroid saponins (digitoxin, deslanoside, ginsenoside Rg1 and Rb1) were investigated to assess the impact of formic acid on the mass response of steroid saponins. Compounds with a conjugated lactonic ring in their structures such as digoxin, digitoxin and deslanoside tended to form stable formate-adduct ions more easily. The LC/MS/MS method developed here is therefore well suited for the quantification of steroid saponins that are difficult to deprotonate using other MS approaches.

Metabolomics investigation of cutaneous T cell lymphoma based on UHPLC-QTOF/MS.

OBJECTIVES: The identification of cutaneous T cell lymphoma (CTCL) biomarkers may serve as a predictor of disease progression and treatment response. The aim of this study was to map potential biomarkers in CTCL plasma. DESIGN AND METHODS: Plasma metabolic perturbations between CTCL cases and healthy individuals were investigated using metabolomics and ultrahigh performance liquid chromatography­quadrupole time-of-flight mass spectrometry (UHPLC-QTOF/MS). RESULTS: Principal component analysis (PCA) of the spectra showed clear metabolic changes between the two groups. Thirty six potential biomarkers associated with CTCL were found. CONCLUSIONS: Based on PCA, several biomarkers were determined and further identified by LC/MS/MS analysis. All of these could be potential early markers of CTCL. In addition, we established that heparin as anticoagulant has better pre-treatment results than EDTA with the UHPLC-QTOF/MS approach.

The large-scale investigation of gene expression in Leymus chinensis stigmas provides a valuable resource for understanding the mechanisms of poaceae self-incompatibility.

BACKGROUND: Many Poaceae species show a gametophytic self-incompatibility (GSI) system, which is controlled by at least two independent and multiallelic loci, S and Z. Until currently, the gene products for S and Z were unknown. Grass SI plant stigmas discriminate between pollen grains that land on its surface and support compatible pollen tube growth and penetration into the stigma, whereas recognizing incompatible pollen and thus inhibiting pollination behaviors. Leymus chinensis (Trin.) Tzvel. (sheepgrass) is a Poaceae SI species. A comprehensive analysis of sheepgrass stigma transcriptome may provide valuable information for understanding the mechanism of pollen-stigma interactions and grass SI. RESULTS: The transcript abundance profiles of mature stigmas, mature ovaries and leaves were examined using high-throughput next generation sequencing technology. A comparative transcriptomic analysis of these tissues identified 1,025 specifically or preferentially expressed genes in sheepgrass stigmas. These genes contained a significant proportion of genes predicted to function in cell-cell communication and signal transduction. We identified 111 putative transcription factors (TFs) genes and the most abundant groups were MYB, C2H2, C3H, FAR1, MADS. Comparative analysis of the sheepgrass, rice and Arabidopsis stigma-specific or preferential datasets showed broad similarities and some differences in the proportion of genes in the Gene Ontology (GO) functional categories. Potential SI candidate genes identified in other grasses were also detected in the sheepgrass stigma-specific or preferential dataset. Quantitative real-time PCR experiments validated the expression pattern of stigma preferential genes including homologous grass SI candidate genes. CONCLUSIONS: This study represents the first large-scale investigation of gene expression in the stigmas of an SI grass species. We uncovered many notable genes that are potentially involved in pollen-stigma interactions and SI mechanisms, including genes encoding receptor-like protein kinases (RLK), CBL (calcineurin B-like proteins) interacting protein kinases, calcium-dependent protein kinase, expansins, pectinesterase, peroxidases and various transcription factors. The availability of a pool of stigma-specific or preferential genes for L. chinensis offers an opportunity to elucidate the mechanisms of SI in Poaceae.