Comparative proteomics analysis of two oat varieties at different developmental stages
Ontology highlight
ABSTRACT: This study explored the molecular mechanisms underlying oat grain development in two oat varieties, Bannister and Bilby, with a focus on lipid biosynthesis.
Project description:Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.
Project description:For proteomic analysis, ADSCs from four independent donors were analyzed (n = 4 biological replicates per condition, OM vs. SM). Cell pellets were lysed in 5% sodium de-oxycholate buffer containing TCEP and CAA, supplemented with protease and phospha-tase inhibitors, followed by sonication and incubation at 60 °C. Protein concentration was determined by BCA assay, and 25 µg of protein was processed with a modified FASP pro-tocol employing 30 kDa filters. After trypsin/LysC digestion, peptides were purified on Waters HLB plates, eluted with 70% acetonitrile/0.1% TFA, dried, and stored at −80 °C. Background: Adipose-derived mesenchymal stem/stromal cells (ADSCs) are gaining recognition in regenerative medicine thanks to their potential for adipogenic, osteogenic, and chondrogenic differentiation, as well as their immunomodulatory properties. How-ever, ADSC-based therapies focus either on differentiation for tissue replacements or on counteracting the unrestrained inflammation to prevent tissue destruction and initiate re-generation. Here, we aim to examine the immunomodulatory potential of osteogenically differentiated ADSCs by analyzing their proteomic profile. Methods: using the LC-MS/MS technique, we created the proteomic profile of differentiated and undifferentiated ADSCs, and compared them with the Reactome database. The transcriptomic analysis was also performed and compared to the proteomic profile. Results: the comparison of proteomic (499 up-regulated; 355 down-regulated) and transcriptomic (212 up-regulated; 232 down-regulated) profiles showed 60,1% concordance – both proteins and transcripts showed the same trend. Significantly upregulated proteins in differentiating ADSCs (−log₁₀ p >5 and >10) were grouped into four categories: propensity for osteogenic differen-tiation; immunomodulation/immune/inflammatory response; cell senescence; cell cycle regulation. Among those proteins, thirteen were reported to play some role in processes such as immunomodulation, inflammatory signaling, transplant rejection, or graft-versus-host disease. Conclusions: we observed that differentiating ADSCs might still exert immunomodulatory effects, which could be used in the treatment of e.g., GvHD.
Project description:Energy densification and enrichment of monounsaturated fatty acids increases oat’s nutritional value among small grain cereals. However, optimization of oat oil traits is challenging through conventional breeding. Using the biolistic method for oat’s oil improvement, here we showed that metabolic engineering is a feasible strategy in improving the oil traits of oat. In this study, two constructs containing three genes involved in lipid biosynthesis pathway (AtWRI1, AtDGAT, and SiOLEOSIN) were transformed into oat cultivar ‘Park’ to enhance the oil composition and content in oat grain and leaves. We performed RNA-sequencing in mature seeds and boot leaves of trasngenic lines. Transgene expression contributed to a global transcriptional reprogramming in oat seeds and leaves. Endogenous DGAT, WRI1, and OLEOSIN genes were up regulated while the genes involved in fatty acid biosynthesis expressed in opposite way between oat seeds and leaves. Transcriptomic studies revealed differential gene expression mainly enriched in lipid metabolism.
Project description:Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat. Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding. Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes. Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.
Project description:Oat endosperm uniquely accumulates oils, differing from other Poaceae crops and oilseed species that primarily store oils in embryos. Different photosynthetic organs' contribution to grain oil accumulation remains unclear. This study investigated the effects of photosynthesis on grain weight and oil accumulation in the ear, flag leaf, and top second leaf of four oat cultivars with varying oil contents, using shading/excision treatments. Studies have shown that ear shading significantly affects grain weight and lipid accumulation in oats. These effects were more pronounced in high-oil cultivars than low-oil cultivars. We further performed transcriptome profiling on the high-oil oat cultivar BY9 at 4 days after ear shading. Transcriptomic analysis indicated that shading altered expression patterns of genes associated with carbohydrate metabolism, fatty acid synthesis, and triacylglycerol assembly. Our findings highlight the critical role of ear photosynthesis in determining both oil production and yield in oats, providing new insights into oil accumulation mechanisms in cereal crops.
Project description:Loiasis, caused by the filarial nematode Loa loa, imposes a significant burden of disease in endemic regions in West and Central Africa. Manifestations include microfilaria in the blood (MF) and migration of the adult eye worm (EW), with clinical presentations ranging from asymptomatic infections to life threatening organ involvement. The diagnostic gold standard, microscopic detection of microfilaria in the blood, remains difficult due to widely varying microfilaria counts, frequent amicrofilaraemia in patients with EW, and unreliable serological assays. By applying high-throughput plasma proteomics, we investigated the human host response in 274 patients with different L. loa disease states (INF), including EW (n=148), MF (n=42), or both (EWMF; n=84), compared to 136 loa-negative (LN) controls. Five proteins were elevated in INF compared to LN, including IGHG3, IGHG4, and LCP1. Four followed the trend from LN to EW to MF and EWMF, reflecting a more pronounced host response to higher microfilaria couMoMoreover, IGHG4 correlated positively with eosinophil and microfilarial counts underlining its role in chronic, parasitic infections. 63 plasma proteins exhibited notable differences depending on self-reported symptoms. The proteomic signature allowed for accurate classification of EW (AUROC = 0.73) and microfilaria positive (0.84) individuals. Together, L. loa infection leads to relevant alterations of the host plasma proteome, highlighting the importance of further in-depth research on this highly neglected parasitic disease. Here, we present additional experiments to validate IGHG4, IGHG3, LCP1, ACTBL2 and IGLV9-49 as proteomic biomarkers for Loa Loa Infection.
Project description:Oats (Avena sativa L.) are a healthy food, being high in dietary fibre (e.g. β-glucans), antioxidants, minerals, and vitamins. Understanding the effect of variety and crop management on nutritional quality is important. The response of four oat varieties to increased nitrogen levels was investigated across multiple locations and years with respect to yield, grain quality and metabolites (assessed via GC- and LC- MS). A novel high-resolution UHPLC-PDA-MS/MS method was developed, providing improved metabolite enrichment, resolution, and identification. The combined phenotyping approach revealed that, amino acid levels were increased by nitrogen supplementation, as were total protein and nitrogen containing lipid levels, whereas health-beneficial avenanthramides were decreased. Although nitrogen addition significantly increased grain yield and β-glucan content, supporting increasing the total nitrogen levels recommended within agricultural guidelines, oat varietal choice as well as negative impacts upon health beneficial secondary metabolites and the environmental burdens associated with nitrogen fertilisation, require further consideration.
Project description:Globally, over 65 million individuals are estimated to suffer from post-acute sequelae of COVID-19 (PASC). A large number of individuals living with PASC experience cardiovascular symptoms (i.e. chest pain and heart palpitations) (PASC-CVS). The role of chronic inflammation in these symptoms, in particular in individuals with symptoms persisting for >1 year after SARS-CoV-2 infection, remains to be determined. Here, we show that compared to individuals with a resolved SARS-CoV-2 infection (and no persistent symptoms), individuals with prolonged PASC-CVS had elevated levels of pro-inflammatory cytokines. However, these cytokines were found to be present in trace amounts, such that they could only be detected with the use of novel nanotechnology. Importantly, these trace-level cytokines had a direct effect on the functionality of primary human cardiomyocytes in vitro. Proteomics analyses demonstrated further differences in PASC-CVS and recovered plasma including increased abundance of complement and coagulation associated proteins.