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Proteomics

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https://www.readbyqxmd.com/read/29194978/a-novel-regulatory-mechanism-for-differentiation-of-mesenchymal-stem-cell-redox-state-of-dj-1-matters
#1
Hideyuki Yamawaki
Reactive oxygen species (ROS) are multifunctional gas transmitter with diverse biologic actions (adverse vs. beneficial) dependent on their level. The differentiation of vascular stem cells into smooth muscle cells (SMCs) might be involved in the pathogenesis of cardiovascular disorders including hypertension and atherosclerosis. Therefore, controlling the differentiation of vascular stem cells is a potential strategy for the treatment of vascular diseases. Nonetheless, it remains to be unrevealed whether ROS could mediate the differentiation of mesenchymal stem cells (MSCs) into SMCs...
December 1, 2017: Proteomics
https://www.readbyqxmd.com/read/29193752/the-proteomic-response-of-b-%C3%A2-pumilus-cells-to-glucose-starvation
#2
Stefan Handtke, Dirk Albrecht, Andreas Otto, Dörte Becher, Michael Hecker, Birgit Voigt
Since starvation for carbon sources is a common condition for bacteria in nature and can also occur in industrial fermentation processes due to mixing zones, knowledge about the response of cells to carbon starvation is beneficial. The preferred carbon source for bacilli is glucose. We analysed the response of B. pumilus cells to glucose starvation using metabolic labelling and quantitative proteomics. Glucose starvation led to an extensive reprogramming of the protein expression pattern in B. pumilus. The amounts of proteins of the central carbon metabolic pathways (glycolysis and TCC) remained stable in starving cells...
November 30, 2017: Proteomics
https://www.readbyqxmd.com/read/29193783/blue-native-sds-page-and-itraq-based-chloroplasts-proteomics-analysis-of-nicotiana-tabacum-leaves-infected-with-m-strain-of-cucumber-mosaic-virus-reveals-several-proteins-involved-in-chlorosis-symptoms
#3
Rong Lei, Zhixin Du, Jun Kong, Guifen Li, Yan He, Yanhong Qiu, Jin Yan, Shuifang Zhu
Virus infection in plants involves necrosis, chlorosis and mosaic. The M strain of cucumber mosaic virus (M-CMV) has six distinct symptoms: vein clearing, mosaic, chlorosis, partial green recovery, complete green recovery and secondary mosaic. Chlorosis indicates the loss of chlorophyll which is highly abundant in plant leaves and plays essential roles in photosynthesis. Blue native/SDS-PAGE combined with mass spectrum was performed to detect the location of virus, and proteomic analysis of chloroplast isolated from virus-infected plants was performed to quantify the changes of individual proteins in order to gain a global view of the total chloroplast protein dynamics during the virus infection...
November 28, 2017: Proteomics
https://www.readbyqxmd.com/read/29178193/proteomic-characterisation-of-caenorhabditis-elegans-larval-development
#4
Tian Xia, Edward R Horton, Anna Elisabetta Salcini, Roger Pocock, Thomas Robert Cox, Janine Terra Erler
The nematode Caenorhabditis elegans is widely used as a model organism to study cell and developmental biology. Quantitative proteomics of C. elegans is still in its infancy and, so far, most studies have been performed on adult worm samples. Here, we used quantitative mass spectrometry to characterise protein level changes across the four larval developmental stages (L1-L4) of C. elegans. In total, we identified 4,130 proteins, and quantified 1,541 proteins that were present across all four stages in three biological replicates from independent experiments...
November 27, 2017: Proteomics
https://www.readbyqxmd.com/read/29152876/refining-transcriptome-gene-catalogs-by-ms-validation-of-expressed-proteins
#5
Sirius P K Tse, Mathieu Beauchemin, David Morse, Samuel C L Lo
Protein sequence identification by tandem mass spectroscopy (LC-MS/MS) identifies thousands of protein sequences even in complex mixtures, and provides valuable insight into the biological functions of different cells. For non-model organisms, transcriptomes are generally used to allow peptide identification, an important addition to their use as a gene catalog allowing the potential metabolic activities of cells to be determined. Here, we used LC-MS/MS data to identify which of the six possible reading frames in the transcriptome was actually used by the cell to make protein, and asked whether this would have an impact on downstream analyses using the transcriptome...
November 19, 2017: Proteomics
https://www.readbyqxmd.com/read/29152854/an-approach-to-incorporate-multi-enzyme-digestion-into-c-tails-for-c-terminomics-studies
#6
Yang Zhang, Qingqing Li, Jingnan Huang, Zhen Wu, Jichang Huang, Lin Huang, Yanhong Li, Juanying Ye, Xumin Zhang
Protein C-termini study is still a challenging task and far behind its counterpart, N-termini study. Mass spectrometry (MS) based C-terminomics study is often hampered by the low ionization efficiency of C-terminal peptides and the lack of efficient enrichment methods. We previously optimized the C-terminal amine-based isotope labeling of substrates (C-TAILS) method and identified 369 genuine protein C-termini in E. coli. A key limitation of C-TAILS is that the prior protection of amines and carboxylic groups at protein level makes Arg-C as the only specific enzyme in practice...
November 19, 2017: Proteomics
https://www.readbyqxmd.com/read/29150981/systematic-proteomic-analysis-of-protein-methylation-in-prokaryotes-and-eukaryotes-revealed-distinct-substrate-specificity
#7
Min Zhang, Jun-Yu Xu, Hao Hu, Bang-Ce Ye, Minjia Tan
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, was largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150926/viral-short-orfs-and-their-possible-functions
#8
REVIEW
Yaara Finkel, Noam Stern-Ginossar, Michal Schwartz
Definition of functional genomic elements is one of the greater challenges of the genomic era. Traditionally, putative short Open Reading Frames (sORFs) coding for less than 100 amino acids were disregarded due to computational and experimental limitations, however it has become clear over the past several years that translation of sORFs is pervasive and serves diverse functions. The development of ribosome profiling, allowing identification of translated sequences genome-wide, revealed wide-spread, previously unidentified translation events...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150924/comprehensive-profiling-of-lysine-acetylome-in-baculovirus-infected-silkworm-bombyx-mori-cells
#9
Dongbing Hu, Shengjie Xue, Cui Zhao, Ming Wei, Huihui Yan, Yanping Quan, Wei Yu
Bombyx mori is one of the key lepidopteran model species, and is economically important for silk production and proteinaceous drug expression. Baculovirus and insect host are important natural biological models for studying host-pathogen interactions. The impact of Bombyx mori nucleopolyhedrovirus (BmNPV) infection on the proteome and acetylome of Bombyx mori ovarian (BmN) cells were explored to facilitate a better understanding of infection-driven interactions between BmNPV and host in vitro. The proteome and acetylome were profiled through 6-plex Tandem mass tag (TMT) labelling-based quantitative proteomics...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29144021/quantitative-extracellular-matrix-proteomics-suggests-cell-wall-reprogramming-in-host-specific-immunity-during-vascular-wilt-caused-by-fusarium-oxysporum-in-chickpea
#10
Eman Elagamey, Kanika Narula, Arunima Sinha, Sudip Ghosh, Magdi A E Abdellatef, Niranjan Chakraborty, Subhra Chakraborty
Extracellular matrix (ECM) is the unique organelle that perceives stress signals and reprograms molecular events of host cell during patho-stress. However, our understanding of how ECM dictates plant immunity is largely unknown. Vascular wilt caused by the soil borne filamentous fungus Fusarium oxysporum is a major impediment for global crop productivity. To elucidate the role of ECM proteins and molecular mechanism associated with cell wall mediated immunity, the temporal changes of ECM proteome was studied in vascular wilt resistant chickpea cultivar upon F...
November 16, 2017: Proteomics
https://www.readbyqxmd.com/read/29136334/identification-of-plasma-membrane-glycoproteins-specific-to-human-glioblastoma-multiforme-cells-using-lectin-arrays-and-lc-ms-ms
#11
YaeEun Park, Jeonghun Yeom, YoungSoo Kim, Hye Jin Lee, Ki-Cheol Han, SeungTaek Lee, Cheolju Lee, Ji Eun Lee
Glioblastoma, also known as glioblastoma multiforme (GBM), is the most malignant type of brain cancer and has poor prognosis with a median survival of less than one year. While the structural changes of tumor cell surface carbohydrates are known to be associated with invasive behavior of tumor cells, the cell surface glycoproteins to differentiate the low- and high-grade glioma cells can be potential diagnostic markers and therapeutic targets for GBMs. In the present study, lectin arrays consisting of eight lectins were employed to explore cell surface carbohydrate expression patterns on low-grade oligodendroglioma cells (Hs683) and GBM cells (T98G)...
November 14, 2017: Proteomics
https://www.readbyqxmd.com/read/29134766/comparative-analyses-of-data-independent-acquisition-mass-spectrometric-approaches-dia-wisim-dia-and-untargeted-dia
#12
Frank Koopmans, Jenny T C Ho, August B Smit, Ka Wan Li
Data independent acquisition (DIA) is an emerging technology for quantitative proteomics. Current DIA focusses on the identification and quantitation of fragment ions that are generated from multiple peptides contained in the same selection-window of several to tens of m/z. An alternative approach is WiSIM-DIA, which combines conventional DIA with wide-SIM (wide-selected ion monitoring) windows to partition the precursor m/z space to produce high quality precursor ion chromatograms. However WiSIM-DIA has been under-explored; it remains unclear if it is a viable alternative to DIA...
November 14, 2017: Proteomics
https://www.readbyqxmd.com/read/29130603/proteogenomic-re-annotation-of-coccidioides-posadasii-strain-silveira
#13
Natalie M Mitchell, Andrew L Sherrard, Surendra Dasari, D Mitchell Magee, Thomas E Grys, Douglas F Lake
The aims of this study were to provide protein-based evidence upon which to re-annotate of the genome of C. posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley Fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira were analyzed using a GeLC-MS/MS method. Acquired spectra were processed with a proteogenomics workflow comprising a Silveira proteome database, a 6-frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs...
November 12, 2017: Proteomics
https://www.readbyqxmd.com/read/29125683/organellar-omics-a-reviving-strategy-to-untangle-the-biomolecular-complexity-of-the-cell
#14
REVIEW
Arun Kumar Tharkeshwar, Kris Gevaert, Wim Annaert
A eukaryotic cell encompasses many membrane-enclosed organelles, each of these holding several types of biomolecules that exhibit tremendous diversity in terms of their localization and expression. Despite the development of increasingly sensitive analytical tools, the enormous biomolecular complexity that exists within a cell cannot yet be fully resolved as low abundant molecules often remain unrecognized. Moreover, a drawback of whole cell analysis is that it does not provide spatial information and therefore it is not capable of assigning distinct biomolecules to specific compartments or analyze changes in the composition of these compartments...
November 10, 2017: Proteomics
https://www.readbyqxmd.com/read/29115712/proteomic-profiling-of-exosomes-secreted-by-breast-cancer-cells-with-varying-metastatic-potential
#15
Lahiru Gangoda, Michael Liem, Ching-Seng Ang, Shivakumar Keerthikumar, Christopher G Adda, Belinda S Parker, Suresh Mathivanan
Cancer cells actively release extracellular vesicles, including exosomes, into the surrounding microenvironment. Exosomes play pleiotropic roles in cancer progression and metastasis, including invasion, angiogenesis, and immune modulation. However, the proteome profile of exosomes isolated from cells with different metastatic potential and the role of these exosomes in driving metastasis remains unclear. Here, we conducted a comparative proteomic analysis of exosomes isolated from several genetically related mouse breast tumour lines with different metastatic propensity...
November 8, 2017: Proteomics
https://www.readbyqxmd.com/read/29110399/de-novo-sequencing-of-peptides-from-high-resolution-bottom-up-tandem-mass-spectra-using-top-down-intended-methods
#16
Kira Vyatkina, Lennard J M Dekker, Si Wu, Martijn M VanDuijn, Xiaowen Liu, Nikola Tolić, Theo M Luider, Ljiljana Paša-Tolić
Despite high-resolution mass spectrometers are becoming accessible for more and more laboratories, tandem (MS/MS) mass spectra are still often collected at a low resolution. And even if acquired at a high resolution, software tools used for their processing do not tend to benefit from that in full, and an ability to specify a relative mass tolerance in this case often remains the only feature the respective algorithms take advantage of. We argue that a more efficient way to analyze high-resolution MS/MS spectra should be with methods more explicitly accounting for the precision level, and sustain this claim through demonstrating that a de novo sequencing framework originally developed for (high-resolution) top-down MS/MS data is perfectly suitable for processing high-resolution bottom-up datasets, even though a top-down like deconvolution performed as the first step will leave in many spectra at most a few peaks...
November 7, 2017: Proteomics
https://www.readbyqxmd.com/read/29106068/global-proteome-analysis-links-lysine-acetylation-to-diverse-functions-in-oryza-sativa
#17
Chao Xue, Shuai Liu, Chen Chen, Jun Zhu, Xibin Yang, Yong Zhou, Rui Guo, Xiaoyu Liu, Zhiyun Gong
Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of lysine acetylation and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localised to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis...
November 6, 2017: Proteomics
https://www.readbyqxmd.com/read/29105980/extracellular-vesicles-in-the-adaptive-process-of-prostate-cancer-during-inhibition-of-androgen-receptor-signalling-by-enzalutamide
#18
Carolina Soekmadji, Anja Rockstroh, Grant A Ramm, Colleen C Nelson, Pamela J Russell
Current treatments for advanced prostate cancer focus on inhibition of the androgen receptor (AR) by androgen deprivation therapy (ADT). However, complex interactions mediated by tumour suppressors, oncogenes, aberrations of AR expression, or de novo androgen production have been shown to induce the adaptive response of prostate cancer, leading to the development of castration resistant prostate cancer (CRPC). In this study, we report the effects of AR antagonist, enzalutamide on the protein contents of extracellular vesicles (EVs)...
November 6, 2017: Proteomics
https://www.readbyqxmd.com/read/29087609/nitrogen-deficiency-induced-alterations-in-the-root-proteome-of-a-pair-of-potato-solanum-tuberosum-l-varieties-contrasting-for-their-response-to-low-n
#19
Anna Maria Jozefowicz, Anja Hartmann, Andrea Matros, Annegret Schum, Hans-Peter Mock
Improving crop nitrogen use efficiency is important both from the economic and the environmental viewpoint. Here, the aim was to highlight differences between the proteomic response of the roots of two potato cultivars contrasting in their response to nitrogen deficiency, in an effort to understand which proteins and metabolic pathways contribute to the tolerance of N deprivation. The two cultivars 'Topas' (tolerant) and 'Lambada' (sensitive) were grown under both an N sufficient and an N deficient regime, using an in vitro- based cultivation system...
October 31, 2017: Proteomics
https://www.readbyqxmd.com/read/29087046/proteomic-screen-of-brain-glycoproteome-reveals-prion-specific-marker-of-pathogenesis
#20
Lise Lamoureux, Sharon L R Simon, Brooks Waitt, J David Knox
Transmissible spongiform encephalopathies (TSEs) are neurodegenerative disorders caused by the presence of an infectious prion protein. The primary site of pathology is the brain characterised by neuroinflammation, astrogliosis, prion fibrils and vacuolation. The events preceding the observed pathology remain in question. We sought to identify biomarkers in the brain of TSE-infected and aged-matched control mice using 2D DIGE. Since the brain proteome is too complex to resolve all proteins using 2D DIGE, protein samples were initially filtered through either concanavalin A (ConA) or wheat-germ agglutinin (WGA) columns...
October 31, 2017: Proteomics
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