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https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#1
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28726080/proteomic-approach-to-address-low-seed-germination-in-cyclobalnopsis-gilva
#2
REVIEW
Madiha Zaynab, Sonia Kanwal, Muhammad Furqan, Waqar Islam, Ali Noman, Ghulam Muhammad Ali, Nazia Rehman, Sara Zafar, Kalsoom Sughra, Muhammad Jahanzab
Seeds play essential roles in plant life cycle and germination is a complex process which is associated with different phases of water imbibition. Upon imbibition, seeds begin utilization of storage substances coupled with metabolic activity and biosynthesis of new proteins. Regeneration of organelles and emergence of radicals lead to the establishment of seedlings. All these activities are regulated in coordinated manners. Translation is the requirement of germination of seeds via involvements of several proteins like beta-amylase, starch phosphorylase...
July 19, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28718811/tissue-specific-labeling-in-proteomics
#3
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/28718403/adam-metalloprotease-released-cancer-biomarkers
#4
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/28717845/proteomics-in-inflammatory-bowel-disease-approach-using-animal-models
#5
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/28717018/structure-and-properties-of-oil-bodies-in-diatoms
#6
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
#7
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/28714877/alternative-pre-mrna-splicing-in-mammals-and-teleost-fish-a-effective-strategy-for-the-regulation-of-immune-responses-against-pathogen-infection
#8
REVIEW
Ming Xian Chang, Jie Zhang
Pre-mRNA splicing is the process by which introns are removed and the protein coding elements assembled into mature mRNAs. Alternative pre-mRNA splicing provides an important source of transcriptome and proteome complexity through selectively joining different coding elements to form mRNAs, which encode proteins with similar or distinct functions. In mammals, previous studies have shown the role of alternative splicing in regulating the function of the immune system, especially in the regulation of T-cell activation and function...
July 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28712655/insulin-regulation-of-proteostasis-and-clinical-implications
#9
REVIEW
Haleigh A James, Brian T O'Neill, K Sreekumaran Nair
Maintenance and modification of the cellular proteome are at the core of normal cellular physiology. Although insulin is well known for its control of glucose homeostasis, its critical role in maintaining proteome homeostasis (proteostasis) is less appreciated. Insulin signaling regulates protein synthesis and degradation as well as posttranslational modifications at the tissue level and coordinates proteostasis at the organism level. Here, we review regulation of proteostasis by insulin in postabsorptive, postprandial, and diabetic states...
July 10, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28712005/an-overview-of-the-ongoing-insights-in-selenium-research-and-its-role-in-fish-nutrition-and-fish-health
#10
REVIEW
Kifayat Ullah Khan, Amina Zuberi, João Batista Kochenborger Fernandes, Imdad Ullah, Huda Sarwar
In the present review, the ongoing researches about selenium research in fish nutrition have been comprehensively discussed. Selenium research is getting popularity in fish nutrition as it is required for the normal growth and proper physiological and biochemical functions in fish. Its deficiency or surplus amounts create severe problems in fish. It is available as inorganic form, organic form, and nano form. In fish, most of the previous research is about the selenium requirements for fish by using only one selenium source mainly the inorganic one...
July 15, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/28709695/peripheral-biomarkers-of-major-depression-and-antidepressant-treatment-response-current-knowledge-and-future-outlooks
#11
REVIEW
Bharathi S Gadad, Manish K Jha, Andrew Czysz, Jennifer L Furman, Taryn L Mayes, Michael P Emslie, Madhukar H Trivedi
BACKGROUND: In recent years, we have accomplished a deeper understanding about the pathophysiology of major depressive disorder (MDD). Nevertheless, this improved comprehension has not translated to improved treatment outcome, as identification of specific biologic markers of disease may still be crucial to facilitate a more rapid, successful treatment. Ongoing research explores the importance of screening biomarkers using neuroimaging, neurophysiology, genomics, proteomics, and metabolomics measures...
July 5, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28706912/diagnosis-and-prognosis-review-of-biomarkers-for-mesothelioma
#12
REVIEW
Huan H Sun, Allen Vaynblat, Harvey I Pass
Malignant pleural mesothelioma (MPM) is an aggressive disease arising in pleural cell lining and is associated with asbestos exposure. Today, there is a rising incidence of MPM reaching 3,000 annual cases nationally, primarily from the large population occupationally exposed to asbestos between 1940 and 1980. With a prolonged latency period, presenting clinically 10 to 40 years after exposure, MPM is often diagnosed in late stages and presents median survival time of less than 12 months. There is a serious need for improvement in prognostic and diagnostic tools for MPM...
June 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28699655/repair-or-destruction-an-intimate-liaison-between-ubiquitin-ligases-and-molecular-chaperones-in-proteostasis
#13
REVIEW
Éva Kevei, Wojciech Pokrzywa, Thorsten Hoppe
Cellular differentiation, developmental processes, and environmental factors challenge the integrity of the proteome in every eukaryotic cell. The maintenance of protein homeostasis, or proteostasis, involves folding and degradation of damaged proteins, and is essential for cellular function, organismal growth, and viability [1, 2]. Misfolded proteins that cannot be refolded by chaperone machineries are degraded by specialized proteolytic systems. A major degradation pathway regulating cellular proteostasis is the ubiquitin/proteasome-system (UPS), which regulates turnover of damaged proteins that accumulate upon stress and during aging...
July 12, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28698834/biomarkers-in-renal-transplantation-an-updated-review
#14
REVIEW
Maurizio Salvadori, Aris Tsalouchos
Genomics, proteomics and molecular biology lead to tremendous advances in all fields of medical sciences. Among these the finding of biomarkers as non invasive indicators of biologic processes represents a useful tool in the field of transplantation. In addition to define the principal characteristics of the biomarkers, this review will examine the biomarker usefulness in the different clinical phases following renal transplantation. Biomarkers of ischemia-reperfusion injury and of delayed graft function are extremely important for an early diagnosis of these complications and for optimizing the treatment...
June 24, 2017: World Journal of Transplantation
https://www.readbyqxmd.com/read/28698311/proteomics-and-metabolomics-in-ageing-research-from-biomarkers-to-systems-biology
#15
REVIEW
Jessica M Hoffman, Yang Lyu, Scott D Pletcher, Daniel E L Promislow
Age is the single greatest risk factor for a wide range of diseases, and as the mean age of human populations grows steadily older, the impact of this risk factor grows as well. Laboratory studies on the basic biology of ageing have shed light on numerous genetic pathways that have strong effects on lifespan. However, we still do not know the degree to which the pathways that affect ageing in the lab also influence variation in rates of ageing and age-related disease in human populations. Similarly, despite considerable effort, we have yet to identify reliable and reproducible 'biomarkers', which are predictors of one's biological as opposed to chronological age...
July 15, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/28695748/proteomic-profiling-of-the-cancer-cell-secretome-informing-clinical-research
#16
Yung-Chin Hsiao, Lichieh Julie Chu, Jen-Ting Chen, Ta-Sen Yeh, Jau-Song Yu
Cancer represents one of the major causes of human deaths. Identification of proteins as biomarkers for early detection of cancer and therapeutic targets for cancer treatment are important issues in precision medicine. Secretome of cancer cells represents the collection of proteins secreted or shed from cancer cells. Proteomic profiling of the cancer cell secretome has been proven to be a convenient and efficient way to discover cancer biomarker and/or therapeutic targets. Areas covered: There have been numerous reviews describing the history and application of secretome analysis in cancer biomarker/therapeutic target research...
July 11, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28694706/abnormalities-in-alternative-splicing-of-angiogenesis-related-genes-and-their-role-in-hiv-related-cancers
#17
REVIEW
Nonkululeko N Mthembu, Zukile Mbita, Rodney Hull, Zodwa Dlamini
Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi's sarcoma, non-Hodgkin's lymphoma, and cervical cancer...
2017: HIV/AIDS: Research and Palliative Care
https://www.readbyqxmd.com/read/28691345/the-skyline-ecosystem-informatics-for-quantitative-mass-spectrometry-proteomics
#18
REVIEW
Lindsay K Pino, Brian C Searle, James G Bollinger, Brook Nunn, Brendan MacLean, Michael J MacCoss
Skyline is a freely available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.
July 9, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28691041/affinity-purification-of-the-rna-degradation-complex-the-exosome-from-hek-293-cells
#19
Michal Domanski, John LaCava
The RNA exosome complex plays a central role in RNA processing and regulated turnover. Present both in cytoplasm and nucleus, the exosome functions through associations with ribonucleases and various adapter proteins (reviewed in [Kilchert et al., 2016]). The following protocol describes an approach to purify RNA exosome complexes from HEK-293 cells, making use of inducible ectopic expression, affinity capture, and rate-zonal centrifugation. The obtained RNA exosomes have been used successfully for proteomic, structural, and enzymatic studies (Domanski et al...
April 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28689450/recent-advances-and-clinical-insights-into-the-use-of-proteomics-in-the-study-of-atherosclerosis
#20
Laura Mourino-Alvarez, Montserrat Baldan-Martin, Raul Rincon, Tatiana Martin-Rojas, Nerea Corbacho-Alonso, Tamara Sastre-Oliva, Maria G Barderas
The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment...
July 10, 2017: Expert Review of Proteomics
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