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Proteomics

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https://www.readbyqxmd.com/read/29457974/a-multi-omics-analysis-of-glycine-max-leaves-reveals-alteration-in-flavonoid-and-isoflavonoid-metabolism-upon-ethylene-and-abscisic-acid-treatment
#1
Ravi Gupta, Cheol Woo Min, Katharina Kramer, Ganesh Kumar Agrawal, Randeep Rakwal, Ki-Hun Park, Yiming Wang, Iris Finkemeier, Sun Tae Kim
Phytohormones are central to the plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves...
February 19, 2018: Proteomics
https://www.readbyqxmd.com/read/29453826/protein-turnover-in-aging-and-longevity
#2
REVIEW
Nathan Basisty, Jesse G Meyer, Birgit Schilling
Progressive loss of proteostasis is a hallmark of aging that is marked by declines in various components of proteostasis machinery, including: autophagy, ubiquitin-mediated degradation, protein synthesis, and others. While declines in proteostasis have historically been observed as changes in these processes, or as bulk changes in the proteome, recent advances in proteomic methodologies have enabled the comprehensive measurement of turnover directly at the level of individual proteins in vivo. These methods, which utilize a combination of stable-isotope labeling, mass spectrometry, and specialized software analysis, have now been applied to various studies of aging and longevity...
February 17, 2018: Proteomics
https://www.readbyqxmd.com/read/29441686/miniaturizing-em-sample-preparation-opportunities-challenges-and-visual-proteomics
#3
REVIEW
Stefan A Arnold, Shirley A Müller, Claudio Schmidli, Anastasia Syntychaki, Luca Rima, Mohamed Chami, H Stahlberg, Kenneth N Goldie, T Braun
This review compares and discusses conventional versus miniaturized specimen preparation methods for transmission electron microscopy (EM). The progress brought by direct electron detector cameras, software developments and automation have transformed transmission cryo-electron microscopy (cryo-EM) and made it an invaluable high-resolution structural analysis tool. In contrast, EM specimen preparation has seen very little progress in the last decades and is now one of the main bottlenecks in cryo-EM. Here, we discuss the challenges faced by specimen preparation for single particle EM, highlight current developments, and show the opportunities resulting from the advanced miniaturized and microfluidic sample grid preparation methods described, such as visual proteomics and time-resolved cryo-EM studies...
February 14, 2018: Proteomics
https://www.readbyqxmd.com/read/29437277/identification-of-native-and-post-translationally-modified-hla-b-57-01-restricted-hiv-envelope-derived-epitopes-using-immunoproteomics
#4
Sri H Ramarathinam, Stephanie Gras, Sheilajen Alcantara, Amanda W S Yeung, Nicole A Mifsud, Secondo Sonza, Patricia T Illing, Elias N Glaros, Robert J Center, Shane Thomas, Stephen J Kent, Nicola Ternette, Damian F J Purcell, Jamie Rossjohn, Anthony W Purcell
The recognition of pathogen-derived peptides by T lymphocytes is the cornerstone of adaptive immunity, whereby intracellular antigens are degraded in the cytosol and short peptides assemble with class I human leukocyte antigen (HLA) molecules in the endoplasmic reticulum (ER). These peptide-HLA complexes egress to the cell surface and are scrutinized by cytotoxic CD8+ T-cells leading to the eradication of the infected cell. Here we identify naturally presented HLA-B*57:01 bound peptides derived from the envelope protein of the human immunodeficiency virus (HIVenv)...
February 13, 2018: Proteomics
https://www.readbyqxmd.com/read/29437267/pharmacoproteomics-profile-in-response-to-acamprosate-treatment-of-an-alcoholism-animal-model
#5
Caroline E Germany, Ashlie N Reker, David J Hinton, Alfredo Oliveros, Xinggui Shen, Lindsey G Andres-Beck, Katheryn M Wininger, Marjan Trutchul, Urska Cvek, Doo-Sup Choi, Hyung W Nam
Acamprosate is an FDA-approved medication for the treatment of alcoholism that is unfortunately only effective in certain patients. Although acamprosate known to stabilize the hyper-glutamatergic state in alcoholism, pharmacological mechanisms of action in brain tissue remains unknown. To investigate the mechanism of acamprosate efficacy, we employed a pharmacoproteomics approach using an animal model of alcoholism, type 1 equilibrative nucleoside transporter (ENT1) null mice. Our results demonstrated that acamprosate treatment significantly decreased both ethanol drinking and preference in ENT1 null mice compared to that of wild-type mice...
February 13, 2018: Proteomics
https://www.readbyqxmd.com/read/29436780/autosomal-tubulointerstitial-kidney-disease-muc1-type-differential-proteomics-suggests-that-mutated-muc1-insc-affects-vesicular-transport-in-renal-epithelial-cells
#6
Simon Staubach, Andrea Wenzel, Bodo B Beck, Markus M Rinschen, Stefan Müller, Franz-Georg Hanisch
Autosomal dominant tubulointerstitial kidney disease associated to the MUC1 gene (ADTKD-MUC1; formerly MCKD1) belongs to a heterogenous group of rare hereditary kidney diseases that is prototypically caused by frameshift mutations in the MUC1 repeat domain. The mutant MUC1(insC) lacks the transmembrane domaine, exhibits aberant cellular topology and hence might gain a function during the pathological process. To get insight into potential pathomechanisms we performed differential proteomics of extracellular vesicles shed by renal epithelia into the urine of patients...
February 13, 2018: Proteomics
https://www.readbyqxmd.com/read/29436760/silac-expands-its-territory-to-the-pathogenic-yeast-candida-albicans
#7
Wooyoung Eric Jang, Min-Sik Kim
Quantitative proteomic analysis using SILAC, as metabolic labeling with mass spectrometry (MS), has been used as an excellent technique to measure relative abundance change in proteins and post-transitional modifications. Since its development in 2002, SILAC has proven to have unique and specific advantage compared to other labeling methods such as iTRAQ and TMT. However, SILAC has limitations in its application to human tissue/organ samples and some types of unicellular organisms that convert supplemented heavy amino acids to others...
February 13, 2018: Proteomics
https://www.readbyqxmd.com/read/29417741/how-can-omic-science-be-improved
#8
Kai Simons
One of the promises of multiomic analysis was to transform the clinical diagnostics to deliver much more exact phenotyping of disease states. However, despite enormous investments, the transformation of clinical routine has not taken place. There are many reasons for this lack of success but one is the failure to deliver quantitative and reproducible data. This failure is not only impeding progress in clinical phenotyping but also in the application of omic science in systems biology. The focus in this Viewpoint will be on lipidomics but the lessons learned are generally applicable...
February 8, 2018: Proteomics
https://www.readbyqxmd.com/read/29412508/proteomics-analysis-of-the-adhesion-activity-of-lactobacillus-acidophilus-atcc-4356-upon-growth-in-an-intestine-like-ph-environment
#9
Zhen Wu, Gang Wang, Wenwen Wang, Daodong Pan, Liuyang Peng, Liwei Lian
Many health effects of Lactobacillus acidophilus are desirable among these the adhesion ability is vital to enhance the possibility of colonization and stabilisation associated with the gut mucosal barrier. In this study, the growth characteristics and the adhesion activity of L. acidophilus in the intestine-like pH environment (pH 7.5) were identified. The number of bacteria adhering to the HT-29 cells was found with a gradual increase trend (pH 5.5-7.5). This also led to the morphological changes of L. acidophilus after exposure to different pH environments...
February 7, 2018: Proteomics
https://www.readbyqxmd.com/read/29409117/comparison-of-secretome-profile-of-pathogenic-and-non-pathogenic-entamoeba-histolytica
#10
Chun-Seob Ahn, Jeong-Geun Kim, Myeong Heon Shin, Young Ah Lee, Yoon Kong
The obligatory intracellular protozoan parasite, Entamoeba histolytica, causes amebic dysentery and liver abscess. E. histolytica adheres to the host tissues in a contact-dependent manner. E. histolytica excretory-secretory products (ESP) might play critical roles during invasion. We comparatively analyzed the secretome profile of E. histolytica pathogenic HM-1:IMSS and non-pathogenic Rahman strains. The two ESP revealed similar but distinct spotting patterns. In both ESP, alcohol dehydrogenase, enolase 1 and transketolase, which control classical carbohydrate metabolism and other moonlighting effects, constituted the most abundant fractions...
February 6, 2018: Proteomics
https://www.readbyqxmd.com/read/29406625/stress-impacts-the-regulation-neuropeptides-in-the-rat-hippocampus-and-prefrontal-cortex
#11
Wenxue Li, Aurelie Papilloud, Laura Lozano-Montes, Nan Zhao, Xuting Ye, Xiaozhe Zhang, Carmen Sandi, Gregor Rainer
Adverse life experience increases the lifetime risk to several stress-related psychopathologies, such as anxiety or depressive-like symptom following stress in adulthood. However, the neurochemical modulations triggered by stress have not been fully characterized. Neuropeptides play an important role as signaling molecules that contribute to physiological regulation and have been linked to neurological and psychiatric diseases. However, little is known about the influence of stress on neuropeptide regulation in the brain...
February 6, 2018: Proteomics
https://www.readbyqxmd.com/read/29405577/impacts-of-dietary-pleurotus-eryngii-polysaccharide-on-nutrient-digestion-metabolism-and-immune-response-of-the-small-intestinal-and-colon-an-itraq-based-proteomic-analysis
#12
Gaoxing Ma, Benard Muinde Kimatu, Liyan Zhao, Wenjian Yang, Fei Pei, Qiuhui Hu
Pleurotus eryngii polysaccharides have been shown to exert significant biological activities to the host. However, few studies have been conducted on its effects on gastrointestinal tract (GIT) health alteration. In the present study, small intestinal and colonic proteome alterations generated by dietary supplementation with a novel homogeneous P. eryngii polysaccharide (PEP) in C57BL/6 mice, based on the isobaric tag for relative and absolute quantification (iTRAQ) proteomics were investigated. Compared to the control group, PEP supplementation resulted in a total of 113 and 194 significant differential proteins (DPs) in the small intestine and colon, respectively...
February 5, 2018: Proteomics
https://www.readbyqxmd.com/read/29393594/the-peptide-repertoire-of-hla-b27-may-include-ligands-with-lysine-at-p2-anchor-position
#13
Shira Yair-Sabag, Valentina Tedeschi, Carolina Vitulano, Eilon Barnea, Fabian Glaser, Dganit Melamed Kadosh, Joel D Taurog, Maria Teresa Fiorillo, Rosa Sorrentino, Arie Admon
The HLA-B*27 peptidome has drawn significant attention due to the genetic association between some of the HLA-B*27 alleles and the inflammatory rheumatic disease Ankylosing Spondylitis (AS), for which a comprehensive biological explanation is still lacking. This study aims to expand the known limits of the HLA-B*27 peptidome to facilitate selection and testing of new peptides, possibly involved in the disease. The HLA peptidomes of HeLa and C1R cell lines stably transfected with the AS-associated HLA-B*27:05 allele, the non-associated HLA-B*27:09 allele, or their Cysteine 67 to Serine mutants (C67S), were analyzed on a very large scale...
February 2, 2018: Proteomics
https://www.readbyqxmd.com/read/29389069/proteomics-with-mass-spectrometry-imaging-beyond-amyloid-typing
#14
Francesca Lavatelli, Giampaolo Merlini
Detection and typing of amyloid deposits in tissues are two crucial steps in the management of systemic amyloidoses. The presence of amyloid deposits is routinely evaluated through Congo red staining, whereas proteomics is now a mainstay for in the identification of the deposited proteins. In this issue of Proteomics, Winter and colleagues describe a novel method based on MALDI mass spectrometry imaging (MALDI-MSI) coupled to ion mobility separation and peptide filtering, to detect the presence of amyloid in histology samples and to identify its composition, while preserving the spatial distribution of proteins in tissues...
February 1, 2018: Proteomics
https://www.readbyqxmd.com/read/29389057/specific-isolation-of-glycoproteins-with-mesoporous-zirconia-polyoxometalate-hybrid
#15
Dandan Zhang, Mengmeng Wang, Zhiyong Guo, Pengfei Guo, Xuwei Chen, Jianhua Wang
A novel mesoporous zirconia-polyoxometalate ZrO2 -P8 W48 hybrid was prepared using a surfactant-assisted solvent evaporation technique. The acid-base reaction between the Zr-OH groups of zirconium oxides and P8 W48 was followed by self-assembly with an amphiphilic triblock copolymer as template to obtain a polyoxometalate-based hybrid. The ZrO2 -P8 W48 hybrid was characterized by Fourier-transform infrared spectroscopy (FT-IR), thermal gravimetric assay (TGA), scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HR-TEM), energy-dispersive X-ray spectroscopy (EDXS), X-ray diffraction (XRD), and nitrogen sorption/desorption...
February 1, 2018: Proteomics
https://www.readbyqxmd.com/read/29384269/17th-chromosome-centric-human-proteome-project-c-hpp-symposium-in-tehran
#16
Anna Meyfour, Sara Pahlavan, Hamid Sobhanian, Ghasem Hosseini Salekdeh
This report describes the 17th Chromosome-Centric Human Proteome Project which was held in Tehran, Iran, April 27-28, 2017. A brief summary of the symposium's talks including new technical and computational approaches for the identification of novel proteins from non-coding genomic regions, physicochemical and biological causes of missing proteins, and the close interactions between C- and B/D-HPP are presented. A synopsis of decisions made on the prospective programs to maintain collaborative works, share resources and information, and establishment of a newly organized working group, the Task Force for Missing Protein Analysis (TAMPA) are discussed...
January 31, 2018: Proteomics
https://www.readbyqxmd.com/read/29377634/in-immunopeptidomics-we-need-a-sniper-instead-of-a-shotgun
#17
Pouya Faridi, Anthony Wayne Purcell, Nathan Paul Croft
Immunopeptidomics employs the use of mass spectrometry to identify and quantify peptides presented on the surface of cells by major histocompatibility complex (MHC; human leukocyte antigen [HLA], in humans) molecules, an essential component of adaptive immunity. Currently, immunopeptidomics follows the same or similar workflows as the more established field of shotgun proteomics, yet inherent differences between these two fields create significant drawbacks for the former. In this viewpoint, we would like to highlight such technical issues and provide suggestions for novel workflows that would increase peptide sequencing coverage, depth, and confidence, collectively enhancing the capabilities of the field of immunopeptidomics...
January 29, 2018: Proteomics
https://www.readbyqxmd.com/read/29369500/insights-from-proteomic-studies-into-plant-somatic-embryogenesis
#18
REVIEW
Angelo Schuabb Heringer, Claudete Santa-Catarina, Vanildo Silveira
Somatic embryogenesis is a biotechnological approach mainly used for the clonal propagation of different plants worldwide. In somatic embryogenesis, embryos arise from somatic cells under appropriate culture conditions. This plasticity in plants is a demonstration of true cellular totipotency and is the best approach among the genetic transformation protocols used for plant regeneration. Despite the importance of somatic embryogenesis, knowledge regarding the control of the somatic embryogenesis process is limited...
January 25, 2018: Proteomics
https://www.readbyqxmd.com/read/29359858/2de-gels-a-story-of-love-and-hate-in-proteomics
#19
Daniel Martins-de-Souza
I think 2DE may still be a very useful proteomic tool. In 2014, we published an article defending the usefulness of 2DE gels in proteomic research [1]. A little earlier, Roepstorff´s group did the same [2].
January 23, 2018: Proteomics
https://www.readbyqxmd.com/read/29359857/proteome-profile-of-american-hybrid-grape-cv-blanc-du-bois-during-ripening-reveals-proteins-associated-with-flavor-volatiles-and-ethylene-production
#20
Devaiah Kambiranda, Sheikh M Basha, Rakesh Singh, Janana Snowden, Roger Mercer
Study of key control points in ripening is essential to improve grape wine quality. Molecular basis of ripening is still far from being understood from the Pierce's disease tolerant grapes predominantly grown in the Southeastern United States. To identify proteins expressed during Blanc Du Bois grape berry green and ripening stages, proteome analysis from five different stages revealed 1091, 1131, 1078, 1042 and 1066 proteins. Differential expression analysis revealed 551 common proteins across different stages of maturity that are involved in various biochemical and metabolic pathways...
January 23, 2018: Proteomics
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