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Proteomics

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https://www.readbyqxmd.com/read/28719664/predicting-the-protein-half-life-in-tissue-from-its-cellular-properties
#1
Mahbubur Rahman, Rovshan G Sadygov
Protein half-life is an important feature of protein homeostasis (proteostasis). The increasing number of in vivo and in vitro studies using high throughput proteomics provide estimates of the protein half-lives in tissues and cells. However, protein half-lives in cells and tissues are different. Due to the resource requirements for researching tissues, more data is available from cellular studies than tissues. We have designed a multivariate linear model for predicting protein half-life in tissue from its cellular properties...
2017: PloS One
https://www.readbyqxmd.com/read/28719652/long-term-follow-up-of-human-t-cell-responses-to-conserved-hiv-1-regions-elicited-by-dna-simian-adenovirus-mva-vaccine-regimens
#2
Nathifa Moyo, Nicola J Borthwick, Edmund G Wee, Silvia Capucci, Alison Crook, Lucy Dorrell, Tomáš Hanke
BACKGROUND: Durability of vaccine-elicited immune responses is one of the key determinants for vaccine success. Our aim is to develop a vaccination strategy against the human immunodeficiency virus type 1 (HIV-1), which induces protective and durable CD8+ T-cell responses. The central theorem of our approach is to focus T cells on highly conserved regions of the HIV-1 proteome and this is achieved through the use of the first-generation conserved vaccine immunogen HIVconsv. This immunogen vectored by plasmid DNA, simian adenovirus and poxvirus MVA was tested in healthy, HIV-1-negative adults in UK and induced high magnitudes of HIVconsv-specific plurifunctional CD8+ T cells capable of in vitro HIV-1 inhibition...
2017: PloS One
https://www.readbyqxmd.com/read/28719635/differential-protein-expression-profile-in-the-hypothalamic-gt1-7-cell-line-after-exposure-to-anabolic-androgenic-steroids
#3
Freddyson J Martínez-Rivera, Juliana Pérez-Laspiur, María E Santiago-Gascot, Abner G Alemán-Reyes, Emanuel García-Santiago, Yolanda Rodríguez-Pérez, Cristhian Calo-Guadalupe, Inelia Otero-Pagán, Roxsana N Ayala-Pagán, Magdiel Martínez, Yisel M Cantres-Rosario, Loyda M Meléndez, Jennifer L Barreto-Estrada
The abuse of anabolic androgenic steroids (AAS) has been considered a major public health problem during decades. Supraphysiological doses of AAS may lead to a variety of neuroendocrine problems. Precisely, the hypothalamic-pituitary-gonadal (HPG) axis is one of the body systems that is mainly influenced by steroidal hormones. Fluctuations of the hormonal milieu result in alterations of reproductive function, which are made through changes in hypothalamic neurons expressing gonadotropin-releasing hormone (GnRH)...
2017: PloS One
https://www.readbyqxmd.com/read/28719341/label-free-quantitative-proteomics-analysis-on-the-cisplatin-resistance-in-ovarian-cancer-cells
#4
F Wang, Y Zhu, S Fang, S Li, S Liu
Quantitative proteomics has been made great progress in recent years. Label free quantitative proteomics analysis based on the mass spectrometry is widely used. Using this technique, we determined the differentially expressed proteins in the cisplatin-sensitive ovarian cancer cells COC1 and cisplatin-resistant cells COC1/DDP before and after the application of cisplatin. Using the GO analysis, we classified those proteins into different subgroups bases on their cellular component, biological process, and molecular function...
May 20, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28719097/mitochondrial-proteostasis-as-a-shared-characteristic-of-slowed-aging-the-importance-of-considering-cell-proliferation
#5
Karyn L Hamilton, Benjamin F Miller
Proteostasis is one of the seven "pillars of aging research" identified by the Trans-NIH Geroscience Initiative and loss of proteostasis is associated with aging and age-related chronic disease. Maintenance of protein turnover represents an important mechanism for preserving proteome fidelity. However, measurement of protein synthesis without consideration for cell proliferation can result in an incomplete picture, devoid of information about how new proteins are being allocated. Simultaneous measurement of protein and DNA synthesis provides critical insight about proteins apportioned for newly proliferating cells versus for somatic maintenance...
July 18, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28719092/what-is-targeted-proteomics-a-concise-revision-of-targeted-acquisition-and-targeted-data-analysis-in-mass-spectrometry
#6
Eva Borràs, Eduard Sabidó
No abstract text is available yet for this article.
July 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28718811/tissue-specific-labeling-in-proteomics
#7
REVIEW
Evelyn Ramberger, Gunnar Dittmar
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed...
July 18, 2017: Proteomes
https://www.readbyqxmd.com/read/28718674/design-and-synthesis-of-a-novel-photoaffinity-probe-for-labelling-egf-receptor-tyrosine-kinases
#8
You-Guang Zheng, Xiao-Qing Wu, Jun Su, Ping Jiang, Liang Xu, Jian Gao, Bin Cai, Min Ji
The epidermal growth factor receptor (EGFR) and HER2 are two important tyrosine kinases that play crucial roles in signal transduction pathways that regulate numerous cellular functions including proliferation, differentiation, migration, and angiogenesis. In the past 20 years, many proteomic methods have emerged as powerful methods to evaluate proteins in biological processes and human disease states. Among them, activity-based protein profiling (ABPP) is one useful approach for the functional analysis of proteins...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28718514/aldehyde-dehydrogenase-1-a1-regulates-energy-metabolism-in-adipocytes-from-different-species
#9
Kefeng Yang, Christopher Adin, Qiwen Shen, Ly James Lee, Lianbo Yu, Paolo Fadda, Arpad Samogyi, Kathleen Ham, Lu Xu, Chen Gilor, Ouliana Ziouzenkova
BACKGROUND: Survival and longevity of xenotransplants depend on immune function and ability to integrate energy metabolism between cells from different species. However, mechanisms for interspecies cross talk in energy metabolism are not well understood. White adipose tissue stores energy and is capable of mobilization and dissipation of energy as heat (thermogenesis) by adipocytes expressing uncoupling protein 1 (Ucp1). Both pathways are under the control of vitamin A metabolizing enzymes...
July 17, 2017: Xenotransplantation
https://www.readbyqxmd.com/read/28718436/trna-modification-is-cancer-having-a-wobble
#10
Francesca Rapino, Sylvain Delaunay, Zhaoli Zhou, Alain Chariot, Pierre Close
Translational control of protein synthesis supports tumor development and progression to metastasis. Wobble tRNA modifications are required during translation elongation and sustain proteome homeostasis. Recent work has highlighted the surprising upregulation of the wobble uridine 34 (U34) tRNA cascade in cancer, which underlies the specific requirement for this pathway in tumor development.
April 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28718403/adam-metalloprotease-released-cancer-biomarkers
#11
REVIEW
Peter Herrlich, Andreas Herrlich
Identification of early cancer, detection of progression, and monitoring of therapeutic success remain urgent issues in clinical medicine, particularly given the increasing cancer incidence in our aging populations. New methodologies have provided enormous progress over the past decades by defining the genetic and proteomic composition of cancers, yielding putative cancer biomarkers detectable in blood or other body fluids less invasively and more cheaply than using currently available screening techniques that often involve biopsies or surgery...
July 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28718225/proteostasis-and-ageing-insights-from-long-lived-mutant-mice
#12
William A Sands, Melissa M Page, Colin Selman
The global increase in life expectancy is creating significant medical, social and economic challenges to current and future generations. Consequently, there is a need to identify the fundamental mechanisms underlying the ageing process. This knowledge should help develop realistic interventions capable of combatting age-related disease, and thus improving late-life health and vitality. While several mechanisms have been proposed as conserved lifespan determinants, the loss of proteostasis- where proteostasis is defined here as the maintenance of the proteome- appears highly relevant to both ageing and disease...
July 17, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28717962/comparative-proteome-analysis-for-identification-of-differentially-abundant-proteins-in-sids
#13
Noha El-Kashef, Iva Gomes, Katja Mercer-Chalmers-Bender, Peter M Schneider, Markus A Rothschild, Martin Juebner
Sudden infant death syndrome (SIDS) remains one of the most common causes of post-neonatal infant mortality in developed countries. Its pathogenesis is still poorly understood. The goal of the present study was to characterize changes in the proteome of SIDS compared to age-matched controls in heart and medulla tissues as well as in blood samples using two complementary quantitative proteomic techniques: 2D-DIGE and iTRAQ aiming to provide new insights into the mechanism of SIDS and to find diagnostic protein patterns...
July 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28717933/a-novel-ms-cleavable-azo-cross-linker-for-peptide-structure-analysis-by-free-radical-initiated-peptide-sequencing-frips
#14
Claudio Iacobucci, Christoph Hage, Mathias Schäfer, Andrea Sinz
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers...
July 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28717845/proteomics-in-inflammatory-bowel-disease-approach-using-animal-models
#15
REVIEW
Fadi H Mourad, Yunki Yau, Valerie C Wasinger, Rupert W Leong
Recently, proteomics studies have provided important information on the role of proteins in health and disease. In the domain of inflammatory bowel disease, proteomics has shed important light on the pathogenesis and pathophysiology of inflammation and has contributed to the discovery of some putative clinical biomarkers of disease activity. By being able to obtain a large number of specimens from multiple sites and control for confounding environmental, genetic, and metabolic factors, proteomics studies using animal models of colitis offered an alternative approach to human studies...
July 17, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28717416/feasibility-of-urinary-extracellular-vesicle-proteome-profiling-using-a-robust-and-simple-clinically-applicable-isolation-method
#16
Irene V Bijnsdorp, Olga Maxouri, Aarzo Kardar, Tim Schelfhorst, Sander R Piersma, Thang V Pham, Andre Vis, R Jeroen van Moorselaar, Connie R Jimenez
Extracellular vesicles (EVs) secreted by prostate cancer (PCa) cells contain specific biomarkers and can be isolated from urine. Collection of urine is not invasive, and therefore urinary EVs represent a liquid biopsy for diagnostic and prognostic testing for PCa. In this study, we optimised urinary EV isolation using a method based on heat shock proteins and compared it to gold-standard ultracentrifugation. The urinary EV isolation protocol using the Vn96-peptide is easier, time convenient (≈1.5 h) and no special equipment is needed, in contrast to ultracentrifugation protocol (>3...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28717018/structure-and-properties-of-oil-bodies-in-diatoms
#17
REVIEW
Yoshiaki Maeda, Daisuke Nojima, Tomoko Yoshino, Tsuyoshi Tanaka
Diatoms accumulate triacylglycerols in spherical organelles called oil bodies when exposed to nutrient deprivation conditions. Oil body biology in diatoms has attracted significant attention due to the complexity of the intracellular organelles and the unique combination of genes generated by the evolutionary history of secondary endosymbiosis. The demand for biofuel production has further increased the interest in and importance of a better understanding of oil body biology in diatoms, because it could provide targets for genetic engineering to further enhance their promising lipid accumulation...
September 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28717016/the-effects-of-phosphorus-limitation-on-carbon-metabolism-in-diatoms
#18
REVIEW
Tore Brembu, Alice Mühlroth, Leila Alipanah, Atle M Bones
Phosphorus is an essential element for life, serving as an integral component of nucleic acids, lipids and a diverse range of other metabolites. Concentrations of bioavailable phosphorus are low in many aquatic environments. Microalgae, including diatoms, apply physiological and molecular strategies such as phosphorus scavenging or recycling as well as adjusting cell growth in order to adapt to limiting phosphorus concentrations. Such strategies also involve adjustments of the carbon metabolism. Here, we review the effect of phosphorus limitation on carbon metabolism in diatoms...
September 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28716668/incomplete-penetrance-in-mitochondrial-optic-neuropathies
#19
Leonardo Caporali, Alessandra Maresca, Mariantonietta Capristo, Valentina Del Dotto, Francesca Tagliavini, Maria Lucia Valentino, Chiara La Morgia, Valerio Carelli
Incomplete penetrance characterizes the two most frequent inherited optic neuropathies, Leber's Hereditary Optic Neuropathy (LHON) and dominant optic atrophy (DOA), due to genetic errors in the mitochondrial DNA (mtDNA) and the nuclear DNA (nDNA), respectively. For LHON, compelling evidence has accumulated on the complex interplay of mtDNA haplogroups and environmental interacting factors, whereas the nDNA remains essentially non informative. However, a compensatory mechanism of activated mitochondrial biogenesis and increased mtDNA copy number, possibly driven by a permissive nDNA background, is documented in LHON; when successful it maintains unaffected the mutation carriers, but in some individuals it might be hampered by tobacco smoking or other environmental factors, resulting in disease onset...
July 14, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28716424/molecular-cloning-of-an-ester-forming-triterpenoid-udp-glucose-28-o-glucosyltransferase-involved-in-saponin-biosynthesis-from-the-medicinal-plant-centella-asiatica
#20
Fernanda de Costa, Carla J S Barber, Yeon-Bok Kim, Darwin W Reed, Haixia Zhang, Arthur G Fett-Neto, Patrick S Covello
Triterpene saponins include bioactive compounds with structures consisting of triterpene aglycones (sapogenins) and one or more sugar moieties linked through acetal or ester glycosidic linkages at one or more sites. Centella asiatica (L.) Urban is a medicinal plant that contains bioactive ursane-type saponins, such as madecassoside and asiaticoside. In this work, glucosylation of triterpenoids in C. asiatica was investigated starting with plant extracts. An enzyme capable of glucosylating asiatic and madecassic acids was partially purified...
September 2017: Plant Science: An International Journal of Experimental Plant Biology
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