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Proteogenomics in Microbiology: Taking the Right Turn at the Junction of Genomics and Proteomics
(Peer reviewed; Journal article, 2014-12)High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of ... -
Proteoglycans contribute to the functional integrity of the glomerular endothelial cell surface layer and are regulated in diabetic kidney disease
(Journal article; Peer reviewed, 2021)All capillary endothelia, including those of the glomeruli, have a luminal cell surface layer (ESL) consisting of glycoproteins, glycolipids, proteoglycans (PGs) and glycosaminoglycans. Previous results have demonstrated ... -
Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia
(Journal article; Peer reviewed, 2020)Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly ... -
Proteomic analysis of formalin-fixed paraffin-embedded glomeruli suggests depletion of glomerular filtration barrier proteins in two-kidney one-clip hypertensive rats
(Peer reviewed; Journal article, 2014-08-16)Background It is well known that hypertension may cause glomerular damage, but the molecular mechanisms involved are still incompletely understood. Methods In the present study, we used formalin-fixed paraffin-embedded ... -
Proteomic Analysis of Mesenchymal Stromal Cells Secretome in Comparison to Leukocyte- and Platelet-Rich Fibrin
(Journal article; Peer reviewed, 2023)Secretomes of mesenchymal stromal cells (MSCs) are emerging as a novel growth factor (GF)-based strategy for periodontal and bone regeneration. The objective of this study was to compare the secretome of human bone marrow ... -
Proteomic analysis of neonatal meningitis-causing Escherichia coli
(Master thesis, 2017-11-30)Meningitis in newborns is a serious infection that causes mortality and neurological injury worldwide. The infection progresses from sepsis, and is dependent on the pathogen being able to cross the blood-brain barrier and ... -
Proteomic analysis of peripheral blood mononuclear cells isolated from patients with pulmonary tuberculosis: A pilot study from Zanzibar, Tanzania
(Journal article; Peer reviewed, 2023)This study aimed at exploring the proteomic profile of PBMCs to predict treatment response in pulmonary tuberculosis (PTB). This was a pilot study conducted among 8 adult patients from Zanzibar, Tanzania with confirmed ... -
Proteomic analysis of total cellular proteins of human neutrophils
(Peer reviewed; Journal article, 2009-08-31)Background: Neutrophils are the most abundant leukocytes in peripheral blood and represent one of the most important elements of innate immunity. Recent subcellular proteomic studies have focused on the identification of ... -
Proteomic Analysis of Zebrafish Protein Recoding via mRNA Editing by ADAR Enzymes
(Journal article; Peer reviewed, 2022)RNA editing by adenosine deaminases of the ADAR family can lead to protein recoding, since inosine formed from adenosine in mRNA is complementary to cytosine; the resulting codon editing might introduce amino acid substitutions ... -
Proteomic analysis unveils Gb3-independent alterations and mitochondrial dysfunction in a gla−/− zebrafish model of Fabry disease
(Journal article; Peer reviewed, 2023)Background Fabry disease (FD) is a rare lysosomal storage disorder caused by mutations in the GLA gene, resulting in reduced or lack of α-galactosidase A activity. This results in the accumulation of globotriaosylceramide ... -
Proteomic and histopathological characterisation of sicca subjects and primary Sjögren’s syndrome patients reveals promising tear, saliva and extracellular vesicle disease biomarkers
(Peer reviewed; Journal article, 2019-07-31)Background Mononuclear cell infiltration of exocrine glands, production of Ro/SSA and La/SSB autoantibodies, along with oral and ocular dryness, are characteristic features of primary Sjögren’s syndrome (pSS). Non-SS sicca ... -
Proteomic Comparison of Bone Marrow Derived Osteoblasts and Mesenchymal Stem Cells
(Journal article; Peer reviewed, 2021)Mesenchymal stem cells (MSCs) can differentiate into osteoblasts, and therapeutic targeting of these cells is considered both for malignant and non-malignant diseases. We analyzed global proteomic profiles for osteoblasts ... -
Proteomic Profiling of Primary Human Acute Myeloid Leukemia Cells Does Not Reflect Their Constitutive Release of Soluble Mediators
(Peer reviewed; Journal article, 2018-12-20)Acute myeloid leukemia (AML) is a heterogeneous disease, and communication between leukemic cells and their neighboring leukemia-supporting normal cells is involved in leukemogenesis. The bone marrow cytokine network is ... -
Proteomic signature of tubulointerstitial tissue predicts prognosis in IgAN
(Journal article; Peer reviewed, 2022-03-24)Background: IgA nephropathy (IgAN) is associated with a significant risk of progression to kidney failure. Tubular atrophy is an established important risk factor for progressive disease, but few studies have investigated ... -
Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid
(Journal article; Peer reviewed, 2021)All-trans retinoic acid (ATRA) and valproic acid (VP) have been tried in the treatment of non-promyelocytic variants of acute myeloid leukemia (AML). Non-randomized studies suggest that the two drugs can stabilize AML and ... -
The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
(Peer reviewed; Journal article, 2012-12)The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some ... -
A proteomics sample metadata representation for multiomics integration and big data analysis
(Journal article; Peer reviewed, 2021)The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding ... -
Proteomics Standards Initiative Extended FASTA Format
(Peer reviewed; Journal article, 2019)Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most ... -
Protocol for a multicentre, parallelgroup, open-label randomised controlled trial comparing ferric carboxymaltose with the standard of care in anaemic Malawian pregnant women: the REVAMP trial
(Journal article; Peer reviewed, 2021)Introduction Anaemia in pregnancy remains a critical global health problem, affecting 46% of pregnant women in Africa and 49% in Asia. Oral iron therapy requires extended adherence to achieve correction of anaemia and ... -
Protocol for data extraction: how realworld data have been used in the National Institute for Health and Care Excellence appraisals of cancer therapy
(Journal article; Peer reviewed, 2022)Introduction Due to the limitations of relying on randomised controlled trials, the potential benefits of real-world data (RWD) in enriching evidence for health technology assessment (HTA) are highlighted. Despite increased ...