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translational proteomics

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https://www.readbyqxmd.com/read/28654069/optimized-protocol-for-the-extraction-of-proteins-from-the-human-mitral-valve
#1
Cristina Banfi, Anna Guarino, Maura Brioschi, Stefania Ghilardi, Valeria Mastrullo, Elena Tremoli, Gianluca Polvani
Analysis of the cellular proteome can help to elucidate the molecular mechanisms underlying diseases due to the development of technologies that permit the large-scale identification and quantification of the proteins present in complex biological systems.The knowledge gained from a proteomic approach can potentially lead to a better understanding of the pathogenic mechanisms underlying diseases, allowing for the identification of novel diagnostic and prognostic disease markers, and, hopefully, of therapeutic targets...
June 14, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28654018/a-quantitative-acetylomic-analysis-of-early-seed-development-in-rice-oryza-sativa-l
#2
Yifeng Wang, Yuxuan Hou, Jiehua Qiu, Zhiyong Li, Juan Zhao, Xiaohong Tong, Jian Zhang
PKA (protein lysine acetylation) is a critical post-translational modification that regulates various developmental processes, including seed development. However, the acetylation events and dynamics on a proteomic scale in this process remain largely unknown, especially in rice early seed development. We report the first quantitative acetylproteomic study focused on rice early seed development by employing a mass spectral-based (MS-based), label-free approach. A total of 1817 acetylsites on 1688 acetylpeptides from 972 acetylproteins were identified in pistils and seeds at three and seven days after pollination, including 268 acetyproteins differentially acetylated among the three stages...
June 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28649883/middle-down-proteomics-a-still-unexploited-resource-for-chromatin-biology
#3
Simone Sidoli, Benjamin A Garcia
Introduction Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac...
June 26, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28649880/understanding-type-1-diabetes-through-proteomics
#4
Inne Crèvecoeur, Saurabh Vig, Chantal Mathieu, Lut Overbergh
Auto-immunity against pancreatic beta-cells leads to an absolute shortage of the hormone insulin, resulting in hyperglycemia and the onset of type 1 diabetes (T1D). Proteomic approaches have been used to elucidate the mechanisms of beta-cell dysfunction and death. Areas covered: In the present review, we discuss discoveries in the beta-cell proteome that have contributed to better insights in the role of the beta-cell in T1D. Techniques, such as 2D-DIGE and MALDI imaging, together with new approaches for sample preparation, including laser capture microdissection and immunopeptidomics, have resulted in novel mechanistic insights in the pathogenesis of T1D...
June 26, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28647089/reverse-phase-protein-arrays-elucidate-mechanisms-of-action-and-phenotypic-response-in-2d-and-3d-models
#5
REVIEW
Michael Pawlak, Neil O Carragher
The development of new 2D and 3D phenotypic screening assays combined with high-throughput genomic and proteomic technologies are well placed to advance a new era of molecular pathway informed Phenotypic Drug Discovery. We describe the application of Reverse Phase Protein Array (RPPA) technology to elucidate the mechanism-of-action of small molecules at the post-translational pathway level. We propose that profiling of phenotypic hits and lead molecules in increasingly more complex 3D in vitro and ex vivo models at the post-translational pathway network level represents an effective strategy to both triage and progress the preclinical development of phenotypic screening hits...
March 2017: Drug Discovery Today. Technologies
https://www.readbyqxmd.com/read/28645873/generation-of-nitric-oxide-by-olive-olea-europaea-l-pollen-during-in-vitro-germination-and-assessment-of-the-s-nitroso-and-nitro-pollen-proteomes-by-computational-predictive-methods
#6
María José Jimenez-Quesada, Rosario Carmona, Elena Lima-Cabello, José Ángel Traverso, Antonio Jesús Castro, M Gonzalo Claros, Juan de Dios Alché
Nitric oxide is recognized as a signaling molecule involved in a broad range of physiological processes in plants including sexual reproduction. NO has been detected in the pollen grain at high levels and regulates pollen tube growth. Previous studies demonstrated that NO as well as ROS are produced in the olive reproductive tissues in a stage- and tissue-specific manner. The aim of this study was to assess the production of NO throughout the germination of olive (Olea europaea L.) pollen in vitro. The NO fluorescent probe DAF-2DA was used to image NO production in situ, which was correlated to pollen viability...
June 20, 2017: Nitric Oxide: Biology and Chemistry
https://www.readbyqxmd.com/read/28645570/quantitative-proteomics-analysis-by-itraq-revealed-underlying-changes-in-thermotolerance-of-arthrospira-platensis
#7
Rong Chang, Bingxin Lv, Bosheng Li
Growth temperature is a critical factor that affects cultivation of Arthrospira platensis which is a type of cyanobacterium widely known as Spirulina that has significant commercial value. To investigate the molecular mechanism underlying the thermotolerance of Spirulina, differential protein expression profiling was carried out using iTRAQ-based quantitative proteomic analysis. This study only analyzed changes in thylakoids. Among the 2085 proteins quantified, 43 differentially expressed proteins were selected based on the fold change cutoff scores of ≥2 or ≤0...
June 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28645290/establishment-of-an-orthotopic-patient-derived-xenograft-mouse-model-using-uveal-melanoma-hepatic-metastasis
#8
Ken Kageyama, Masahiro Ohara, Kengo Saito, Shinji Ozaki, Mizue Terai, Michael J Mastrangelo, Paolo Fortina, Andrew E Aplin, Takami Sato
BACKGROUND: Metastatic uveal melanoma is a highly fatal disease; most patients die from their hepatic metastasis within 1 year. A major drawback in the development of new treatments for metastatic uveal melanoma is the difficulty in obtaining appropriate cell lines and the lack of appropriate animal models. Patient-derived xenograft (PDX) tumor models, bearing ectopically implanted tumors at a subcutaneous site, have been developed. However, these ectopically implanted PDX models have obstacles to translational research, including a low engraftment rate, slow tumor growth, and biological changes after multiple passages due to the different microenvironment...
June 23, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28644433/ctla-4-mediated-posttranslational-modifications-direct-cytotoxic-t-lymphocyte-differentiation
#9
Holger Lingel, Josef Wissing, Aditya Arra, Denny Schanze, Stefan Lienenklaus, Frank Klawonn, Mandy Pierau, Martin Zenker, Lothar Jänsch, Monika C Brunner-Weinzierl
The blockade of inhibitory receptors such as CTLA-4 (CD152) is being used as immune-checkpoint therapy, offering a powerful strategy to restore effective immune responses against tumors. To determine signal components that are induced under the control of CTLA-4 we analyzed activated murine CD8(+) T cells by quantitative proteomics. Accurate mass spectrometry revealed that CTLA-4 engagement led to central changes in the phosphorylation of proteins involved in T-cell differentiation. Beside other targets, we discovered a CTLA-4-mediated induction of the translational inhibitor programmed cell death-4 (PDCD4) as a result of FoxO1 nuclear re-localization...
June 23, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28642470/quantitative-proteomics-analysis-reveals-novel-targets-of-mir-21-in-zebrafish-embryos
#10
Ying Wu, Qi-Yong Lou, Feng Ge, Qian Xiong
MicroRNAs (miRNAs) are noncoding RNAs which control gene expression by the suppression of translation or the degradation of mRNAs. Dre-miR-21 (miR-21) has been reported to impact cardiac valvulogenesis in zebrafish embryos. However, the target genes of miR-21 are still largely unknown. Here a tandem isobaric mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-21-regulated proteins. A total of 251 proteins were dysregulated after miR-21 knockdown, suggesting that they may be regulated by miR-21...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28633045/mrna-transport-local-translation-in-neurons
#11
REVIEW
Caspar Glock, Maximilian Heumüller, Erin M Schuman
Neurons are amongst the most structurally complex cells and exhibit a high degree of spatial compartmentalization. Also, neurons exhibit rapid and dynamic signaling by processing information in a precise and, sometimes, spatially-restricted manner. The signaling that occurs in axons and dendrites necessitates the maintenance and modification of their local proteomes. Local translation of mRNAs into protein is one solution that neurons use to meet synaptic demand and activity. Here we review some of the key findings and recent discoveries that have shaped our understanding of local translation in neuronal function and highlight important new techniques that might pave the way for new insights...
June 17, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28632924/metabolomics-as-a-driver-in-advancing-precision-medicine-in-sepsis
#12
Michelle Eckerle, Lilliam Ambroggio, Michael Puskarich, Brent Winston, Alan E Jones, Theodore J Standiford, Kathleen A Stringer
OBJECTIVE: The objective of this review is to explain the science of metabolomics-a science of systems biology that measures and studies endogenous small molecules (metabolites) that are present in a single biological sample-and its application to the diagnosis and treatment of sepsis. In addition, we discuss how discovery through metabolomics can contribute to the development of precision medicine targets for this complex disease state and the potential avenues for those new discoveries to be applied in the clinical environment...
June 20, 2017: Pharmacotherapy
https://www.readbyqxmd.com/read/28630811/development-of-a-branched-radio-frequency-ion-trap-for-electron-based-dissociation-and-related-applications
#13
Takashi Baba, J Larry Campbell, J C Yves Le Blanc, Paul R S Baker, James W Hager, Bruce A Thomson
Collision-induced dissociation (CID) is the most common tool for molecular analysis in mass spectrometry to date. However, there are difficulties associated with many applications because CID does not provide sufficient information to permit details of the molecular structures to be elucidated, including post-translational-modifications in proteomics, as well as isomer differentiation in metabolomics and lipidomics. To face these challenges, we are developing fast electron-based dissociation devices using a novel radio-frequency ion trap (i...
2017: Mass Spectrometry
https://www.readbyqxmd.com/read/28629911/combined-mass-spectrometry-imaging-and-top-down-microproteomics-reveals-evidence-of-a-hidden-proteome-in-ovarian-cancer
#14
Vivian Delcourt, Julien Franck, Eric Leblanc, Fabrice Narducci, Yves-Marie Robin, Jean-Pascal Gimeno, Jusal Quanico, Maxence Wisztorski, Firas Kobeissy, Jean-François Jacques, Xavier Roucou, Michel Salzet, Isabelle Fournier
BACKGROUND: Recently, it was demonstrated that proteins can be translated from alternative open reading frames (altORFs), increasing the size of the actual proteome. Top-down mass spectrometry-based proteomics allows the identification of intact proteins containing post-translational modifications (PTMs) as well as truncated forms translated from reference ORFs or altORFs. METHODS: Top-down tissue microproteomics was applied on benign, tumor and necrotic-fibrotic regions of serous ovarian cancer biopsies, identifying proteins exhibiting region-specific cellular localization and PTMs...
June 3, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28629792/alternative-splicing-and-start-sites-lessons-from-the-grainyhead-like-family
#15
REVIEW
Lee B Miles, Sebastian Dworkin, Charbel Darido
The two main mechanisms that expand the proteomic output of eukaryotic genes are alternative splicing and alternative translation initiation signals. Despite being essential to generate isoforms of gene products that create functional diversity during development, the impact of these mechanisms on fine-tuning regulatory gene networks is still underappreciated. In this review, we use the Grainyhead-like (Grhl) family as a case study to illustrate the importance of isoforms when investigating transcription factor family function during development and disease, and highlight the potential for differential modulation of downstream target genes...
June 16, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28626463/cereal-crop-proteomics-systemic-analysis-of-crop-drought-stress-responses-towards-marker-assisted-selection-breeding
#16
REVIEW
Arindam Ghatak, Palak Chaturvedi, Wolfram Weckwerth
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28626361/molecular-biomarkers-of-colorectal-cancer-and-cancer-disparities-current-status-and-perspective
#17
Upender Manne, Trafina Jadhav, Balananda-Dhurjati Kumar Putcha, Temesgen Samuel, Shivani Soni, Chandrakumar Shanmugam, Esther A Suswam
This review provides updates on the efforts for the development of prognostic and predictive markers in colorectal cancer based on the race/ethnicity of patients. Since the clinical consequences of genetic and molecular alterations differ with patient race and ethnicity, the usefulness of these molecular alterations as biomarkers needs to be evaluated in different racial/ethnic groups. To accomplish personalized patient care, a combined analysis of multiple molecular alterations in DNA, RNA, microRNAs (miRNAs), metabolites, and proteins in a single test is required to assess disease status in a precise way...
December 2016: Current Colorectal Cancer Reports
https://www.readbyqxmd.com/read/28625053/annotation-of-the-domestic-pig-genome-by-quantitative-proteogenomics
#18
Harald Marx, Hannes Hahne, Susanne E Ulbrich, Angelika Schnieke, Oswald Rottmann, Dimitrij Frishman, Bernhard Kuster
The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step towards the comprehensive understanding of porcine biology, evolution and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the functional and structural annotation of the Sus scrofa genome is far from complete. Here, we present mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 to 39 days after gestation...
June 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28624627/histopathological-and-proteomic-responses-in-male-chinese-rare-minnow-gobiocypris-rarus-indicate-hepatotoxicity-following-benzotriazole-exposure
#19
Xuefang Liang, Jinmiao Zha, Christopher J Martyniuk, Zijian Wang, Ji Zhao
Benzotriazole (BT) and its associated derivatives are used ubiquitously in industrial processes, and can be detected in indoor temperature coolants and in chemicals designed to inhibit corrosion. This chemical has been widely detected in aquatic environments and shows some degree of environmental persistence. Evidence has shown that BT exposure can negatively affect endocrine systems and can result in neurotoxicity in fish. However, no study has examined whether this chemical exhibits hepatotoxicity in fish, and if so, what are the underlying mechanism associated with the damage...
June 15, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28624519/itraq-based-quantitative-proteomics-analysis-of-molecular-mechanisms-associated-with-bombyx-mori-lepidoptera-larval-midgut-response-to-bmnpv-in-susceptible-and-near-isogenic-strains
#20
Haizhong Yu, Xueyang Wang, Jiaping Xu, Yan Ma, Shangzhi Zhang, Dong Yu, Dongqiong Fei, Azharuddin Muhammad
Bombyx mori nucleopolyhedrovirus (BmNPV) has been identified as a major pathogen responsible for severe economic loss. Most silkworm strains are susceptible to BmNPV, with only a few highly resistant strains thus far identified. Here we investigated the molecular basis of silkworm resistance to BmNPV using susceptible (the recurrent parent P50) and resistant (near-isogenic line BC9) strains and a combination of iTRAQ-based quantitative proteomics, reverse-transcription quantitative PCR and Western blotting...
June 14, 2017: Journal of Proteomics
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