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https://www.readbyqxmd.com/read/29353021/phosphoproteomics-unveils-stable-energy-supply-as-key-to-flooding-tolerance-in-kandelia-candel
#1
Dezhuo Pan, Lingxia Wang, Fanglin Tan, Si Lu, Xiaojie Lv, Madiha Zaynab, Chi-Lien Cheng, Yakubu Saddeeq Abubakar, Shipin Chen, Wei Chen
The mangrove Kandelia candel (L.) Druce experiences daily flooding cycles. To explore the molecular mechanism underlying the physiological adaptation of K. candel to flooding, the potential role of protein phosphorylation in flooding responses was investigated by a large-scale quantitative phosphoproteomic analysis using isobaric tag for relative and absolute quantitation. Total 2141 unique phosphopeptides and 2603 non-redundant phosphorylation sites were identified from 1516 phosphoproteins in K. candel leaves...
January 15, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29351836/interrogating-interactions-and-modifications-of-histones-in-live-cells
#2
Xiao-Meng Li, Xiang David Li
In this issue of Cell Chemical Biology, new methods are reported to interrogate histone interactions and modifications. Kleiner et al. (2018) develop a chemical proteomics platform for profiling of direct, context-dependent histone-protein interactions in living cells, and Delachat et al. (2018) engineer fluorescent sensors for coexisting histone modifications in live stem cells.
January 18, 2018: Cell Chemical Biology
https://www.readbyqxmd.com/read/29351208/preservation-method-and-phosphate-buffered-saline-washing-affect-the-acute-myeloid-leukemia-proteome
#3
Rebecca Wangen, Elise Aasebø, Andrea Trentani, Stein-Ove Døskeland, Øystein Bruserud, Frode Selheim, Maria Hernandez-Valladares
Acute myeloid leukemia (AML) primary cells can be isolated from peripheral blood, suspended with media containing bovine serum and cryoprotectant, and stored in liquid nitrogen before being processed for proteomic analysis by mass spectrometry (MS). The presence of bovine serum and human blood proteins in AML samples can hamper the identifications of proteins, and thereby reduce the proteome coverage of the study. Herein, we have established the effect of phosphate buffered saline (PBS) washing on AML patient samples stored in media...
January 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29349874/assessment-by-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-of-the-effects-of-preanalytical-variables-on-serum-peptidome-profiles-following-long-term-sample-storage
#4
Sachio Tsuchida, Mamoru Satoh, Hiroshi Umemura, Kazuyuki Sogawa, Masaki Takiwaki, Takayuki Ishige, Yui Miyabayashi, Yuuya Iwasawa, Sohei Kobayashi, Minako Beppu, Motoi Nishimura, Yoshio Kodera, Kazuyuki Matsushita, Fumio Nomura
PURPOSE: Human serum and plasma are often used as clinical specimens in proteomics analyses, and peptidome profiling of human serum is a promising tool for identifying novel disease-associated biomarkers. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for peptidomic biomarker discovery. Careful sample collection and handling are required as either can have a profound impact on serum peptidome patterns, yet the effects of preanalytical variables on serum peptidome profiles have not been completely elucidated...
January 19, 2018: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29348127/murine-chronic-graft-versus-host-disease-proteome-profiling-discovers-ccl15-as-a-novel-biomarker-in-patients
#5
Jing Du, Ryan Flynn, Katelyn Paz, Hong-Gang Ren, Yuko Ogata, Qing Zhang, Philip R Gafken, Barry E Storer, Nathan H Roy, Janis K Burkhardt, Wendy Mathews, Jakub Tolar, Stephanie J Lee, Bruce R Blazar, Sophie Paczesny
Improved diagnostic and treatment methods are needed for chronic graft-versus-host disease (cGVHD), the leading cause of late non-relapse mortality (NRM) in long-term survivors of allogenic hematopoietic cell transplantation (allo-HCT). Validated biomarkers that facilitate disease diagnosis, and classification generally are lacking in cGVHD. Here, we conducted whole serum proteomics analysis of a well-established murine multi-organ system cGVHD model. We discovered 4 up-regulated proteins during cGVHD that are targetable by genetic ablation or blocking antibodies, including the RAS and JUN kinase activator, CRKL, and CXCL7, CCL8 and CCL9 chemokines...
January 18, 2018: Blood
https://www.readbyqxmd.com/read/29347914/in-depth-proteomic-analysis-of-boar-spermatozoa-through-shotgun-and-gel-based-methods
#6
Jean M Feugang, Shengfa F Liao, Scott T Willard, Peter L Ryan
BACKGROUND: Mature spermatozoa contain numerous epididymal and seminal plasma proteins, which full identification through high-throughput technologies may allow for a better understanding of the sperm biology. Therefore, we conducted a global proteomic analysis of boar spermatozoa through shotgun and gel-based methodologies. RESULTS: The total proteins were extracted from mature spermatozoa and subjecsted to proteome analyses. Functional analyses of gene ontology representations and pathway enrichments were conducted on the shotgun dataset, followed by immunology and gene expression validations...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29347346/elucidating-distinct-ion-channel-populations-on-the-surface-of-hippocampal-neurons-via-single-particle-tracking-recurrence-analysis
#7
Grzegorz Sikora, Agnieszka Wyłomańska, Janusz Gajda, Laura Solé, Elizabeth J Akin, Michael M Tamkun, Diego Krapf
Protein and lipid nanodomains are prevalent on the surface of mammalian cells. In particular, it has been recently recognized that ion channels assemble into surface nanoclusters in the soma of cultured neurons. However, the interactions of these molecules with surface nanodomains display a considerable degree of heterogeneity. Here, we investigate this heterogeneity and develop statistical tools based on the recurrence of individual trajectories to identify subpopulations within ion channels in the neuronal surface...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346409/prediction-of-absolute-risk-of-acute-graft-versus-host-disease-following-hematopoietic-cell-transplantation
#8
Catherine Lee, Sebastien Haneuse, Hai-Lin Wang, Sherri Rose, Stephen R Spellman, Michael Verneris, Katharine C Hsu, Katharina Fleischhauer, Stephanie J Lee, Reza Abdi
Allogeneic hematopoietic cell transplantation (HCT) is the treatment of choice for a variety of hematologic malignancies and disorders. Unfortunately, acute graft-versus-host disease (GVHD) is a frequent complication of HCT. While substantial research has identified clinical, genetic and proteomic risk factors for acute GVHD, few studies have sought to develop risk prediction tools that quantify absolute risk. Such tools would be useful for: optimizing donor selection; guiding GVHD prophylaxis, post-transplant treatment and monitoring strategies; and, recruitment of patients into clinical trials...
2018: PloS One
https://www.readbyqxmd.com/read/29345424/a-fluorescence-based-sensor-assay-that-monitors-general-protein-aggregation-in-human-cells
#9
Marisa Pereira, Diogo Tomé, Ana S Domingues, Ana S Varanda, Cristiana Paulo, Manuel A S Santos, Ana R Soares
Protein conformational disorders are characterized by disruption of protein folding and toxic accumulation of protein aggregates. Here we describe a sensitive and simple method to follow and monitor general protein aggregation in human cells. Heat shock protein 27 (HSP27) is an oligomeric small heat shock protein that binds and keeps unfolded proteins in a folding competent state. This high specificity of HSP27 for aggregated proteins can be explored to monitor aggregation in living cells by fusing it to a fluorescent protein as Green Fluorescent Protein (GFP)...
January 18, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29344964/recent-advances-and-opportunities-in-proteomic-analyses-of-tumor-heterogeneity
#10
REVIEW
Nicholas W Bateman, Thomas P Conrads
Solid tumor malignancies comprise a highly variable admixture of tumor and non-tumor cellular populations, forming a complex cellular ecosystem and tumor microenvironment. This tumor heterogeneity is not incidental and is known to correlate with poor patient prognosis for many cancer types. Indeed, non-malignant cell populations, such as vascular endothelial and immune cells, are known to play key roles supporting and, in some cases, driving aggressive tumor biology and represent targets of emerging therapeutics, such as anti-angiogenesis and immune checkpoint inhibitors...
January 17, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344888/perseus-a-bioinformatics-platform-for-integrative-analysis-of-proteomics-data-in-cancer-research
#11
Stefka Tyanova, Juergen Cox
Mass spectrometry-based proteomics is a continuously growing field marked by technological and methodological improvements. Cancer proteomics is aimed at pursuing goals such as accurate diagnosis, patient stratification, and biomarker discovery, relying on the richness of information of quantitative proteome profiles. Translating these high-dimensional data into biological findings of clinical importance necessitates the use of robust and powerful computational tools and methods. In this chapter, we provide a detailed description of standard analysis steps for a clinical proteomics dataset performed in Perseus, a software for functional analysis of large-scale quantitative omics data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344883/discovering-altered-regulation-and-signaling-through-network-based-integration-of-transcriptomic-epigenomic-and-proteomic-tumor-data
#12
Amanda J Kedaigle, Ernest Fraenkel
With the extraordinary rise in available biological data, biologists and clinicians need unbiased tools for data integration in order to reach accurate, succinct conclusions. Network biology provides one such method for high-throughput data integration, but comes with its own set of algorithmic problems and needed expertise. We provide a step-by-step guide for using Omics Integrator, a software package designed for the integration of transcriptomic, epigenomic, and proteomic data. Omics Integrator can be found at http://fraenkel...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344869/isolation-of-amyloid-plaques-and-neurofibrillary-tangles-from-archived-alzheimer-s-disease-tissue-using-laser-capture-microdissection-for-downstream-proteomics
#13
Eleanor Drummond, Shruti Nayak, Geoffrey Pires, Beatrix Ueberheide, Thomas Wisniewski
Here, we describe a new method that allows localized proteomics of amyloid plaques and neurofibrillary tangles (NFTs), which are the two pathological hallmarks of Alzheimer's disease (AD). Amyloid plaques and NFTs are visualized using immunohistochemistry and microdissected from archived, formalin-fixed paraffin-embedded (FFPE) human tissue samples using laser-capture microdissection. The majority of human tissue specimens are FFPE; hence the use of this type of tissue is a particular advantage of this technique...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344863/the-isolation-of-pure-populations-of-neurons-by-laser-capture-microdissection-methods-and-application-in-neuroscience
#14
Renée Morris, Prachi Mehta
In mammals, the central nervous system (CNS) is constituted of various cellular elements, posing a challenge to isolating specific cell types to investigate their expression profile. As a result, tissue homogenization is not amenable to analyses of motor neurons profiling as these represent less than 10% of the total spinal cord cell population. One way to tackle the problem of tissue heterogeneity and obtain meaningful genomic, proteomic, and transcriptomic profiling is to use laser capture microdissection technology (LCM)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344853/laser-microdissection-based-microproteomics-of-formalin-fixed-and-paraffin-embedded-ffpe-tissues
#15
Rémi Longuespée, Dominique Baiwir, Gabriel Mazzucchelli, Nicolas Smargiasso, Edwin De Pauw
Laser microdissection-based proteomics on formalin-fixed and paraffin-embedded tissues is usually performed from relatively large tissue areas or pools of multiple tissue pieces. However, several molecular pathology studies require working on very limited amounts of tissue. This is for example the case when very early cancer lesions have to be handled. Hereby, we present a method for the processing of very small pieces of formalin-fixed and paraffin-embedded tissues for proteomic purposes. This approach is designed in order to avoid sample loss during technical processing and to optimize the digestion of tissue areas containing as little as 2700 cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344848/current-status-and-future-possibilities-of-molecular-genetics-techniques-in-brassica-napus
#16
REVIEW
Muhammad Afzal, Salem Safer Alghamdi, Muhammad Habib Ur Rahman, Awais Ahmad, Tahir Farooq, Mukhtar Alam, Imtiaz Ali Khan, Hidayat Ullah, Wajid Nasim, Shah Fahad
As PCR methods have improved over the last 15 years, there has been an upsurge in the number of new DNA marker tools, which has allowed the generation of high-density molecular maps for all the key Brassica crop types. Biotechnology and molecular plant breeding have emerged as a significant tool for molecular understanding that led to a significant crop improvement in the Brassica napus species. Brassica napus possess a very complicated polyploidy-based genomics. The quantitative trait locus (QTL) is not sufficient to develop effective markers for trait introgression...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29344294/cardiomyocyte-restricted-low-density-lipoprotein-receptor-related-protein-6-lrp6-deletion-leads-to-lethal-dilated-cardiomyopathy-partly-through-drp1-signaling
#17
Zhidan Chen, Yang Li, Ying Wang, Juying Qian, Hong Ma, Xiang Wang, Guoliang Jiang, Ming Liu, Yanpeng An, Leilei Ma, Le Kang, Jianguo Jia, Chunjie Yang, Guoping Zhang, Ying Chen, Wei Gao, Mingqiang Fu, Zheyong Huang, Huiru Tang, Yichun Zhu, Junbo Ge, Hui Gong, Yunzeng Zou
Low density lipoprotein receptor-related protein 6 (LRP6), a wnt co-receptor, regulates multiple functions in various organs. However, the roles of LRP6 in the adult heart are not well understood. Methods: We observed LRP6 expression in heart with end-stage dilated cardiomyopathy (DCM) by western blot. Tamoxifen-inducible cardiac-specific LRP6 knockout mouse was constructed. Hemodynamic and echocardiographic analyses were performed to these mice. Results: Cardiac LRP6 expression was dramatically decreased in patients with end-stage dilated cardiomyopathy (DCM) compared to control group...
2018: Theranostics
https://www.readbyqxmd.com/read/29343144/cell-surface-proteomics-for-the-identification-of-novel-therapeutic-targets-in-cancer
#18
Laura Kuhlmann, Emma Cummins, Ismael Samudio, Thomas Kislinger
Cancer is the second most common cause of death worldwide and its heterogeneity complicates therapy. Standard cytotoxic regiments disrupt rapidly dividing cells, regardless of their neoplastic status. The introduction of less toxic targeted therapies has partially contributed to the observed decrease in cancer-related mortality. Cell-surface proteins represent attractive targets for therapy, due to their easily-accessible localization and their involvement in essential signaling pathways, often dysregulated in cancer...
January 18, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29343059/top-down-characterization-of-heavily-modified-histones-using-193-nm-ultraviolet-photodissociation-uvpd-mass-spectrometry
#19
Sylvester M Greer, Jennifer S Brodbelt
The characterization of protein post-translational modifications (PTMs) remains a significant challenge for traditional bottom-up proteomics methods owing to the lability of PTMs and the difficulty of mapping combinatorial patterns of PTMs based on analysis of small peptides. These shortcomings have accelerated interest in top-down MS/MS methods which focus on analysis of intact proteins. Mapping all protein PTMs simultaneously requires the ability to obtain extensive sequence coverage to allow confident localization of the modifications...
January 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29341164/patient-derived-organoid-models-help-define-personalized-management-of-gastrointestinal-cancer
#20
REVIEW
M R Aberle, R A Burkhart, H Tiriac, S W M Olde Damink, C H C Dejong, D A Tuveson, R M van Dam
BACKGROUND: The prognosis of patients with different gastrointestinal cancers varies widely. Despite advances in treatment strategies, such as extensive resections and the addition of new drugs to chemotherapy regimens, conventional treatment strategies have failed to improve survival for many tumours. Although promising, the clinical application of molecularly guided personalized treatment has proven to be challenging. This narrative review focuses on the personalization of cancer therapy using patient-derived three-dimensional 'organoid' models...
January 2018: British Journal of Surgery
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