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: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: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.
Project description:Two varieties of turmeric, FMO (Fat Mild Orange) and TYA (Thin Yellow Aromatic) were compared. Rhizomes were harvested 3, 5, and 7 months after planting, roots were harvested at 7 months, and leaves were harvested at 7 months. Plants were grown under controlled conditions in the greenhouse.
Project description:A novel henipavirus (HNV) named Langya virus (LayV) was isolated in human patients in China in August 2022. It is closely related to Mòjiāng virus (MojV) and represents the first instance of HNV zoonosis to humans outside of Nipah virus (NiV) and Hendra viruses (HeV). Within this work, mass spectrometry glycoproteomic analysis revealed that although the LayV F protein has reduced glycosylation compared to its NiV and HeV counterparts, a unique glycan was identified positioned at the DIII apex, shielding a previously identified site of vulnerability in NiV F.
Project description:Cuticular waxes coating leaf surfaces can help tolerate drought events by reducing non-stomatal water loss. Despite their role in drought tolerance, little is known about the cuticular wax responses of Canadian bread wheat varieties. To fill in this gap, RNAseq was performed on the flag leaf of four modern varieties to identify potential markers that could be used for selection of higher accumulation of cuticular waxes. This analysis revealed that the W1 locus is a good candidate for higher accumulation of β-diketones.