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Article
Open AccessHAS3-induced extracellular vesicles from melanoma cells stimulate IHH mediated c-Myc upregulation via the hedgehog signaling pathway in target cells
Intercellular communication is fundamental to the survival and maintenance of all multicellular systems, whereas dysregulation of communication pathways can drive cancer progression. Extracellular vesicles (EV...
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Article
Open AccessSimple 3D culture of dissociated kidney mesenchyme mimics nephron progenitor niche and facilitates nephrogenesis Wnt-independently
Kidney mesenchyme (KM) and nephron progenitors (NPs) depend on WNT activity, and their culture in vitro requires extensive repertoire of recombinant proteins and chemicals. Here we established a robust, simple cu...
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Article
Open AccessCaspase-2 and p75 neurotrophin receptor (p75NTR) are involved in the regulation of SREBP and lipid genes in hepatocyte cells
Lipid-induced toxicity is part of several human diseases, but the mechanisms involved are not fully understood. Fatty liver is characterized by the expression of different growth and tissue factors. The neurot...
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Article
Open AccessSETBP1 induces transcription of a network of development genes by acting as an epigenetic hub
SETBP1 variants occur as somatic mutations in several hematological malignancies such as atypical chronic myeloid leukemia and as de novo germline mutations in the Schinzel–Giedion syndrome. Here we show that ...
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Article
Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells
Human SH-SY5Y neuroblastoma cells are widely utilized in in vitro studies to dissect out pathogenetic mechanisms of neurodegenerative disorders. These cells are considered as neuronal precursors and differenti...
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Article
Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules
Neuronal ceroid lipofuscinoses (NCL) are the most commonly inherited progressive encephalopathies of childhood. Pathologically, they are characterized by endolysosomal storage with different ultrastructural fe...
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Label-Free LC-MS/MS Comparative Analysis of Protein S-Nitrosome in Synaptosomes from Wild-Type and APP Transgenic Mice
Posttranslational S-nitrosylation (SNO) of cysteine thiols in proteins is one of the important mechanisms of nitric oxide-based signaling in vivo. A role for protein S-nitrosylation has been proposed in differ...
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Protocol
MALDI-Imaging Mass Spectrometry on Tissues
Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)—profiling and imaging mass spectrometry (MSI) are promising technologies for measuring hundreds of different molecules directly on tissues...
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Article
Open AccessThe Arctic AβPP mutation leads to Alzheimer’s disease pathology with highly variable topographic deposition of differentially truncated Aβ
The Arctic mutation (p.E693G/p.E22G)fs within the β-amyloid (Aβ) region of the β-amyloid precursor protein gene causes an autosomal dominant disease with clinical picture of typical Alzheimer’s disease. Here w...
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Article
Translation of HTT mRNA with expanded CAG repeats is regulated by the MID1–PP2A protein complex
Expansion of CAG repeats is a common feature of various neurodegenerative disorders, including Huntington’s disease. Here we show that expanded CAG repeats bind to a translation regulatory protein complex cont...
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Article
An empirical framework for binary interactome map**
A framework based on numerous empirical data, including protein-protein interaction reference sets, provides parameters for assessing the quality and coverage of protein-protein interaction datasets and estima...
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Article
Open AccessAnalytical model of peptide mass cluster centres with applications
The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate peptide mass lists, to ...
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Article
Open AccessTransformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process
Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is called a peak-list. In or...
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Article
Open AccessCalibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants
Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra...
