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21.
Benjamin C. Blum Weiwei Lin Matthew L. Lawton Qian Liu Julian Kwan Isabella Turcinovic Ryan Hekman Pingzhao Hu Andrew Emili 《Molecular & cellular proteomics : MCP》2022,21(1):100189
Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings. 相似文献
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S. T. Zakhidov T. L. Marshak E. A. Malolina A. Yu. Kulibin I.A. Zelenina S. M. Pavluchenkova V. M. Rudoi O. V. Dement’eva S. G. Skuridin Yu. M. Evdokimov 《Biochemistry (Moscow) Supplemental Series A: Membrane and Cell Biology》2010,4(3):293-296
The effect of gold nanoparticles on mouse epididymal sperm has been studied using the model system of nuclear chromatin decondensation
in vitro. It is shown that the treatment of gametes, preliminary membrane-freed by sodium dodecyl sulfate, in the mediums
containing gold nanoparticles (with diameter ∼2.5 nm) in concentrations 1.0 × 1015 or 0.5 × 1015 particles/ml and following incubation in dithiothreitol solution (DTT) resulted in failure of chromatin decondensation process
and nucleus structure. We conclude that gold nanoparticles possess spermatotoxicity. The mechanism of cytotoxic effect of
gold nanoparticles may be related with their interaction with molecules of double-helix DNA. The model system studied in this
research is applicable for further investigations of cytotoxic effects of nanoparticles of different origin and made of different
metals. 相似文献
25.
Okadaic acid (OA), a protein phosphatase inhibitor, was found to induce hyperphosphorylation and reorganization of vimentin intermediate filaments in 9L rat brain tumor cells. The process was dose dependent. Vimentin phosphorylation was initially enhanced by 400 nM OA in 30 min and reached maximal level (about 26-fold) when cells were treated with 400 nM OA for 90 min. Upon removal of OA, dephosphorylation of the hyperphosphorylated vimentin was observed and the levels of phosphorylation returned to that of the controls after the cells recovered under normal growing conditions for 11 h. The phosphorylation and dephosphorylation of vimentin induced by OA concomitantly resulted in reversible reorganization of vimentin filaments and alteration of cell morphology. Cells rounded up as they were entering mitosis in the presence of OA and returned to normal appearance after 11 h of recovery. Immuno-staining with anti-vimentin antibody revealed that vimentin filaments were disassembled and clustered around the nucleus when the cells were treated with OA but subsequently returned to the filamentous states when OA was removed. Two-dimensional electrophoresis analysis further revealed that hyperphosphorylation of vimentin generated at least seven isoforms having different isoelectric points. Furthermore, the enhanced vimentin phosphorylation was accompanied by changes in the detergent-solubility of the protein. In untreated cells, the detergent-soluble and -insoluble vimentins were of equal amounts but the solubility could be increased when vimentins were hyperphosphorylated in the presence of OA. Taken together, the results indicated that OA could be involved in reversible hyperphosphorylation and reorganization of vimentin intermediate filaments, which may play an important role in the structure-function regulation of cytoskeleton in the cell. 相似文献
26.
Biophysics - HMGB1 is one of the key proteins of the cell. HMGB1 performs its main functions predominantly in the cell nucleus, as an essential component of DNA–protein and multiprotein... 相似文献
27.
Naumova E. V. Vladimirov Yu. A. Beloussov L. V. Tuchin V. V. Volodyaev I. V. 《Biophysics》2021,66(5):764-778
Biophysics - This review is devoted to the methods for studying the ultraweak luminescence of biological objects; in addition to modern methods aimed at studies in the visible, near-infrared, and... 相似文献
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E. P. Isakova Yu. I. Deryabina N. N. Gessler T. A. Belozerskaya Ya. M. Rabinovich 《Applied Biochemistry and Microbiology》2010,46(3):318-323
Cell respiratory activity of protoplasts obtained from the wild type of Neurospora crassa and photoreceptor complex WCC—white collar 1 (wc-1) and white collar 2 (wc-2)—mutants of Neurospora crassa strains was investigated. Respiration inhibition by KCN in the presence of 25 mM succinate was similar in all strains and
did not exceed 83–85% against control. The significant induction of KCN-resistant respiratory pathway occurred under 1% glucose
oxidation in wc-1 and wc-2 mutants if compared with the wild type strains. The inhibitors of the main (cytochrome) pathway of electron transfer in mitochondria—1
mM KCN and antimycin A (4 μg/ml)—blocked the respiration rate of the protoplasts from N. crassa wild type by 75%, while the cell respiration of wc-1 and wc-2 strains was suppressed by approximately 50%. The specific inhibitor of alternative oxidase—10 mM salicylhydroxamic acid (SHAM)—in
combination with the blockers of mitochondrial electron transfer chain caused the total suppression of respiratory activity
of protoplasts in all studied strains. It is supposed that an increase of KCN-resistance in WCC mutants under glucose oxidation
is connected with alternative oxidase activation as the result of failure in reception and signal transduction of active oxygen
species. 相似文献