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ProteomicsHDL functionality is dependent on hepatocyte stress defense factors NRF1 and NRF2
High density lipoproteins (HDL) promote homeostasis and counteract stressful tissue damage that underlie cardiovascular and other diseases by mediating reverse cholesterol transport, reducing inflammation, and abrogating oxidative damage. However, metabolically stressful conditions associated with a...
ORGANISM(S): Mus musculus (Mouse) 
2023-07-03 | PXD042103 | Pride
High density lipoprotein  liver stress defense  cholesterol  transcription factor  immunometabolism 
ProteomicsEPIC: Software Toolkit for Elution Profile-Based Inference of Protein Complexes
Heteromeric protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to preci...
ORGANISM(S): Caenorhabditis elegans 
2019-07-16 | PXD011182 | Pride
Cf/ms  epic  biochemical fractionation  worm interaction network  mass spectrometry  proteomics  protein complexes 
ProteomicsAmorphous silica nanoparticle exposures can lead to mitochondrial protein changes
Mitochondrial fractions from J774 mouse macrophage/monocyte cells were exposed to amorphous silica nanoforms and mitochondrial protein profiles were examined to gain information on relative toxicities of these nanomaterials on mitochondrial pathways and identify potency determinants, for risk charac...
ORGANISM(S): Mus musculus (Mouse) 
2023-03-22 | PXD027593 | Pride
Proteomics Mass spectrometry Exposure Physicochemical characteristics Mitochondria Amorphous silica nanomaterials Nanoforms 
ProteomicsA Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Molecular Determinants in Redox Homeostasis and NF-κB Signaling
Mitochondrial protein (MP) dysfunction has been linked to neurodegenerative disorders (NDs), however, the discovery of molecular mechanisms underlying NDs has been impeded by the limited characterization of interactions governing MP function. Here, using 109 affinity-purified mitochondrial fractions...
ORGANISM(S): Homo sapiens (Human) 
2017-12-05 | PXD006690 | Pride
Parkinson's disease Autism Mitochondria Nf-kb signaling Mitochondrial proteins Neurodegeneration Protein-protein interactions Proteomics 
ProteomicsHuman-Soybean Allergies: Elucidation of the Seed Proteome & Comprehensive PPI Prediction
In this work, a total of eight proteins have been identified (six specific to the human proteome and two specific to the soybean proteome) that are supported by literature to be involved in human health, specifically related to immunological and neurological pathways. Our approach involved the use o...
ORGANISM(S): Glycine max 
2023-03-22 | PXD023875 | Pride
Human Ppi Pipe Allergy Seed protein Glycine max Ms/ms spectra Soybean Computational biology 
ProteomicsThe Conserved Tpk1 Regulates Non-Homologous End Joining Double-Strand Break Repair by Phosphorylation of Nej1, a Homolog of the Human XLF
The yeast cyclic-AMP dependent protein kinase A (PKA) is a ubiquitous serine-threonine kinase, encompassing three catalytic (Tpk1-3) and one regulatory (Bcy1) subunits. Evidence suggests PKA involvement in DNA damage checkpoint response, but how DNA repair pathways are regulated by PKA subunits rema...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-09-10 | PXD024695 | Pride
Genomic instability Prkacb Nhej Tpk1 Dsb repair Nej1 Kinase 
ProteomicsThe Conserved Tpk1 Regulates Non-Homologous End Joining Double-Strand Break Repair by Phosphorylation of Nej1, a Homolog of the Human XLF
The yeast cyclic-AMP dependent protein kinase A (PKA) is a ubiquitous serine-threonine kinase, encompassing three catalytic (Tpk1-3) and one regulatory (Bcy1) subunits. Evidence suggests PKA involvement in DNA damage checkpoint response, but how DNA repair pathways are regulated by PKA subunits rema...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-09-10 | PXD024768 | Pride
Genomic instability Prkacb Nhej Tpk1 Dsb repair Nej1 Kinase 
ProteomicsMitochondrial Network Organization during Neuronal Reprogramming, MT_UDF_SEC
The study focuses on an extensive biochemical fractionation with in-depth quantitative mass spectrometric profiling in the mitochondrial (mt) extracts of cultured human NTera2 embryonal carcinoma stem cells (i.e. ECSCs or undifferentiated state) and upon exposure to retinoic acid-induced differentia...
ORGANISM(S): Homo sapiens (Human) 
2020-01-09 | PXD009834 | Pride
Biochemical fractionation  ci and civ deficiencies  differentiated neuronal cells  human ntera2 embryonal carcinoma stem cells  mass spectrometry  mitochondrial proteins  mitochondrial interaction landscape  proteomics  protein complexes  patient fibroblasts  neurodegeneration  orphans 
ProteomicsMitochondrial Network Organization during Neuronal Reprogramming, MT-DF-WAX
The study focuses on an extensive biochemical fractionation with in-depth quantitative mass spectrometric profiling in the mitochondrial (mt) extracts of cultured human NTera2 embryonal carcinoma stem cells (i.e. ECSCs or undifferentiated state) and upon exposure to retinoic acid-induced differentia...
ORGANISM(S): Homo sapiens (Human) 
2020-01-09 | PXD009831 | Pride
Biochemical fractionation  ci and civ deficiencies  differentiated neuronal cells  human ntera2 embryonal carcinoma stem cells  mass spectrometry  mitochondrial proteins  mitochondrial interaction landscape  proteomics  protein complexes  patient fibroblasts  neurodegeneration  orphans 
ProteomicsMitochondrial Network Organization during Neuronal Reprogramming, MT_DF_SEC
The study focuses on an extensive biochemical fractionation with in-depth quantitative mass spectrometric profiling in the mitochondrial (mt) extracts of cultured human NTera2 embryonal carcinoma stem cells (i.e. ECSCs or undifferentiated state) and upon exposure to retinoic acid-induced differentia...
ORGANISM(S): Homo sapiens (Human) 
2020-01-09 | PXD009833 | Pride
Biochemical fractionation  ci and civ deficiencies  differentiated neuronal cells  human ntera2 embryonal carcinoma stem cells  mass spectrometry  mitochondrial proteins  mitochondrial interaction landscape  proteomics  protein complexes  patient fibroblasts  neurodegeneration  orphans 
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