Control and LgG4 binding proteins
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Hela Cell
SUBMITTER: 
Chuwei Lin
LAB HEAD: Sixue Chen
PROVIDER: PXD030528 | Pride | 2024-04-30
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Control.msf | Msf | |||
| Control_1.raw | Raw | |||
| Control_2.raw | Raw | |||
| Control_3.raw | Raw | |||
| checksum.txt | Txt |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:Mitogen-activated protein kinase 4 (MPK4) was first identified as a negative regulator of systemic acquired resistance (SAR). It is also an important kinase that gets involved in other plant biological processes in plants, including cytokinesis, reproduction and photosynthesis. Arabidopsis thaliana mpk4 mutant is a dwarf and sterile. Previous ‘omics’ studies including genomics, transcriptomics and proteomics have revealed new functions of MPK4 in different biological processes. However, due to challenges in metabolomics, no study has focused on metabolomic profiles of the mpk4 mutant and what metabolites and metabolic pathways are potentially regulated by MPK4 are not known. Metabolites are crucial components of plants, which plays an and they play important roles in plant signaling, defense, and growth and development. Here we used targeted and untargeted metabolomics to profile metabolites in wild type (WT) and the mpk4 mutant where we found that in addition to jasmonic acid (JA) and salicylic acid (SA) pathways, MPK4 got involved in polyamine synthesis and photosynthesis. In addition, we also conducted label-free proteomics of the two genotypes. Integration of metabolomics and proteomics data allowed insight into the metabolomic networks that are potentially regulated by MPK4.
2022-02-15 | PXD030175 | Pride
Project description:Proteins from Hela cells were captured by monosaccharide and disaccharide probes. Resulting proteins were went through proteomics. Unique proteins from disaccharide samples were selected for further research.
2024-04-30 | PXD030471 | Pride
Project description:Plants are often challenged by numerous biotic and abiotic environmental stresses. They have evolved efficient signaling networks in response to the environmental challenges, such as pathogen invasion, drought, CO2 changes. Guard cells are specialized epidermal cells enclosing pores on leaf surface, aka, stomata. Stomatal guard cells are at the frontline of biotic and abiotic stress responses. The opening and closing of stomata are regulated by a sophisticated intracellular signaling networks. Mitogen-activated protein kinase 4 (MPK4) was first identified as negative regulator in systemic acquired resistance (SAR). It was also play important roles in cytokinesis, reproduction, and photosynthesis. MPK4 has higher expression levels in plant guard cells than in mesophyll cells. Arabidopsis mpk4 mutant has higher levels of salicylic acid (SA) and reactive oxygen species (ROS), which are related with stomatal movement. The specific function of MPK4 in guard cells is unknown. In order to understand MPK4 functions in guard cells, it is essential to investigate MPK4-associated protein complex. Here we focus on identification of guard cell specific MPK4 complex using affinity purification following by mass spectrometry (AP-MS). Potential substrates were selected and validated with yeast two hybrid (Y2H).
2024-04-30 | PXD034347 | Pride
Project description:Mesembryanthemum crystallinum (common ice plant) is a facultative halophyte species, which has adapted to extreme conditions. In this study, we cloned a McHB7 transcription factor gene from the ice plant. The expression of McHB7 was significantly induced by 500 mM NaCl and it reached the peak under salt treatment for 7 days. The McHB7 protein was targeted to the nucleus. Overexpression of McHB7 gene in ice plant leaves by Agrobacterium-mediated transformation led to 25 times more McHB7 transcripts than the non-transformed control wild type (WT). After 500 mM NaCl treatment for 7 days, SOD, POD activities and water content of the transgenic plants were significantly higher than WT, while MDA content was decreased in the transgenic plants. Proteomics results showed that a total of 1082 and 1072 proteins were profiled under control and salt treatment, respectively. 22 (2%) and 11 (1%) proteins were uniquely identified under control and salt stress conditions, respectively. Among these 11 proteins, 7 were increased and 4 were decreased. Most identified proteins involved in the processes of regulation of biological, transporter and catalytic activity, biosynthesis of secondary metabolties and response to stimulus were significantly increased in the McHB7 overexpression ice plants under high salinity. All the results demonstrate that the McHB7 transcription factor plays a positive role in improving plant salt tolerance.
2022-02-17 | PXD025961 | Pride
Project description:To determine whether and how warming affects the functional capacities of the active microbial communities, GeoChip 5.0 microarray was used. Briefly, four fractions of each 13C-straw sample were selected and regarded as representative for the active bacterial community if 16S rRNA genes of the corresponding 12C-straw samples at the same density fraction were close to zero.
2023-12-30 | E-MTAB-13326 | biostudies-arrayexpress
Project description:Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained in the Center for Environmental Biotechnology at the University of Tennessee. Fish husbandry, spawning, and experimental procedures were conducted with approval from the University of Tennessee Institutional Animal Care and Use Committee (Protocol #1690-1007). Water for holding fish and conducting experiments (hereafter referred to as fish water) consisted of MilliQ water (Millipore, Bedford, MA) with ions added: 19 mg/L NaHCO3, 1 mg/L sea salt (Instant Ocean Synthetic Sea Salt, Mentor, OH), 10 mg/L CaSO4, 10 mg/L MgSO4, 2 mg/L KCl. Embryos were obtained by spawning adult fish with no history of contaminant exposure. Fertilization of embryos took place at the same time (± 15 min.), such that larvae used in experiments were of similar age at the time of exposure. All activities (maintenance of adult fish, spawning, and experiments) were conducted in an environmental chamber with a temperature of 27± 1 ºC and 14:10h light:dark photoperiod. Experiment Overall Design: At 72 h post-fertilization, zebrafish larvae were exposed to lyophilized Microcystis and purified MC-LR at concentrations of 100 and 1,000 µg/L. Controls consisted of zebrafish system water (negative control) and zebrafish system water containing 0.05% ethanol (vehicle control). Larvae from both control groups as well as 100 µg/L MC-LR, 1,000 µg/L MC-LR, and lyophilized Microcystis were exposed in groups of 50 with three replicates and were sacrificed after 96 hours for total RNA extraction and subsequent microarray analysis. All larvae were exposed in beakers containing 100 ml of solution. Experiment Overall Design: Water samples for microcystin analysis and water quality measurements were taken during the experiment, and mortality and behavioral observations were recorded at 24-hour intervals. Microcystin analysis was conducted by protein phosphatase inhibition assay. Measured concentrations of microcystin-LR were 140 ± 12 SD (low concentration) and 1,703 ± 71 SD (high concentration). The concentration of microcystin-LR in the lyophilized Microcystis treatment was 4.5 µg/L. Water quality parameters measured included dissolved oxygen (6.7 mg/L), pH (6.9), total alkalinity (36 mg/L as CaCO3), total hardness (18 mg/L as CaCO3), and ammonia (<0.2 mg/L). No significant mortality or behavioral changes in larvae were observed during the exposure.
2009-08-07 | E-GEOD-12214 | biostudies-arrayexpress
Project description:Hepatocellular carcinoma (HCC) accounts for approximately 90% of primary liver cancers, the second leading cause of cancer mortality worldwide. Although HCC surgical treatment may be curative in the early stages, its five-year overall survival is only 50-70%. Advances in proteomic technologies have expanded the breadth and depth of cancer proteome characterization. Here, we present the largest characterization effort on proteomic profiling of 222 tumor and paired non-tumor tissues in clinically early HCC (Barcelona Clinic Liver Cancer (BCLC) stage 0 and A). Quantitative proteomic data identified three more-refined subtypes in the early- stage cohort of HCC (termed S-I, S-II and S-III) with different clinical outcomes. S-I retained hepatic detoxification and metabolic functions with the best prognosis, S-II increased molecular expression related to proliferation, and S-III showed distinct enrichment of tumor metastasis and immune response pathways and the poorest prognosis. The subtype specific signatures targeted by known FDA approved drugs or inhibitors under clinical investigations for HCC provide a novel resource for HCC therapeutic targets. A new mechanism of disrupted cholesterol homeostasis with aberrant accumulation of cholesteryl esters was also highlighted in S-III. Thus, this study represents the first proteomic stratification of early-stage HCC, providing insights into tumor biology and personalized targeted therapy.
2019-03-01 | PXD008373 | Pride
Project description:Asthma and postinfectious bronchiolitis obliterans (PIBO) are chronic lung diseases characterized by recurrent episodes of wheezing. Mycoplasma, adenovirus, and respiratory syncytial virus infections can trigger both asthma and PIBO. These two diseases have common etiologic mechanisms that cause airway epithelial injury. They are often difficult to differentiate clinically in preschool children because both are exacerbated by viral infections and respond similarly to steroids and β2 agonists. PIBO, which is occasionally observed in children, is diagnosed through characteristic findings of air trapping on computed tomography or in biopsy samples of lung tissue. However, researchers have not clearly identified the specific blood markers that can distinguish these diseases or the differences in the mechanisms of development. We performed proteomic analysis of plasma to identify specific biomarkers that can be helpful in differentiating asthma from PIBO. This study discovered plasma biomarker candidates by measuring plasma proteome sequential window acquisition of all theoretical mass spectra (SWATH-MS) and included 30 healthy children, 18 with asthma and 15 with PIBO. was used to measure proteins in plasma samples. We identified and quantified 354 proteins across all 63 samples in the SWATH-MS analysis.
2022-12-01 | PXD034996 | Pride
Project description:The Arabidopsis MAP kinase 4 (MPK4) has been proposed as negative player in plant immunity, but it is activated by pathogen-associated molecular patterns (PAMPs), such as flg22. The molecular mechanisms by which MPK4 is activated and controls plant defense remain elusive. In this study, we investigated the Arabidopsis defense against a bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 when the MPK4 is overexpressed. We showed an increase in pathogen resistance and suppression of jasmonic acid (JA) signaling in the MPK4 overexpressing (OE) plants. We also showed that the OE plants are very sensitive to flg22-triggered reactive oxygen species (ROS) burst in guard cells, which resulted in an enhanced stomatal closure, compared to wild-type (WT). During the flg22 activation, dynamic phosphorylation of MPK4 within and outside of the conserved TEY activation loop was observed. To elucidate how MPK4 functions during the defense response, we used immunoprecipitation coupled with mass spectrometry (IP-MS) to identify MPK4 interacting proteins in the absence and presence of flg22. Quantitative proteomic analysis revealed a shift in MPK4-associated protein network, providing insight into the molecular functions of MPK4 at a systems level.
2019-01-14 | PXD009016 | Pride
Project description:The GASH/Sal hamster (Genetic audiogenic seizure, Salamanca) is a model of audiogenic seizures with the epileptogenic focus localized in the inferior colliculus (IC). The sound-induced seizures exhibit a short latency (7-9 seconds), which implies innate protein disturbances in the IC as a basis for seizure susceptibility and generation. Here, we aim to study the protein profile in the GASH/Sal IC in comparison to controls. Protein samples from the IC were processed for enzymatic digestion and then analyzed by mass spectrometry in Data-Independent Acquisition mode. After identifying the proteins using the UniProt database, we selected those with differential expression. We identified 5254 proteins, of which 184 were differentially expressed, 126 upregulated and 58 downregulated. Moreover, a small number of proteins were uniquely found in the GASH/Sal or the control. The resuls indicated a protein profile alteration in the epileptogenic nucleus that might underlie the innate occuring audiogenic seizures in the GASH/Sal model.
2023-05-10 | PXD039755 | Pride