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https://www.readbyqxmd.com/read/29029129/a-visual-review-of-the-human-pathogen-streptococcus-pneumoniae
#1
Ditte Høyer Engholm, Mogens Kilian, David S Goodsell, Ebbe Sloth Andersen, Rikke Schmidt Kjærgaard
Being the principal causative agent of bacterial pneumonia, otitis media, meningitis and septicemia, the bacterium Streptococcus pneumoniae is a major global health problem. To highlight the molecular basis of this problem, we have portrayed essential biological processes of the pneumococcal life cycle in eight watercolor paintings. The paintings are done to a consistent nanometer scale based on currently available data from structural biology and proteomics. In this review article, the paintings are used to provide a visual review of protein synthesis, carbohydrate metabolism, cell wall synthesis, cell division, teichoic acid synthesis, virulence, transformation and pilus synthesis based on the available scientific literature within the field of pneumococcal biology...
October 5, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29026209/wd40-repeat-domain-proteins-a-novel-target-class
#2
REVIEW
Matthieu Schapira, Mike Tyers, Maricel Torrent, Cheryl H Arrowsmith
Antagonism of protein-protein interactions (PPIs) with small molecules is becoming more feasible as a therapeutic approach. Successful PPI inhibitors tend to target proteins containing deep peptide-binding grooves or pockets rather than the more common large, flat protein interaction surfaces. Here, we review one of the most abundant PPI domains in the human proteome, the WD40 repeat (WDR) domain, which has a central peptide-binding pocket and is a member of the β-propeller domain-containing protein family...
October 13, 2017: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/29025360/best-practice-of-identification-and-proteomic-analysis-of-extracellular-vesicles-in-human-health-and-disease
#3
Barbara W Sódar, Árpád Kovács, Tamás Visnovitz, Éva Pállinger, Károly Vékey, Gabriella Pocsfalvi, Lilla Turiák, Edit I Buzás
Extracellular vesicles are emerging sources of biomarkers for modern preventive and precision medicine. Extracellular vesicles in body fluids offer a unique opportunity for integrative biomarker approaches due to their complex biocargo that includes proteins, lipids, nucleic acids and metabolites. Mass spectrometry-based proteomics data suggest that a significant portion of human proteins are sorted into extracellular vesicles and amenable for biomarker discovery schemes. Areas covered: this review focuses on key aspects of isolation, quality control and subsequent analysis of blood plasma- and conditioned medium-derived extracellular vesicle proteins, and summarizes the current state-of-the-art in the field...
October 13, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29025353/mass-spectrometry-based-proteomics-analyses-in-kallikrein-related-peptidase-research-implications-for-cancer-research-and-therapy
#4
Lakmali Munasinghage Silva, Judith Ann Clements
Kallikrein-related peptidases (KLKs) are a family of serine peptidases that are deregulated in numerous pathological conditions, with a multitude of KLK-mediated functional roles implicated in the progression of cancer. Advances in multidimensional mass spectrometry (MS)-based proteomics have facilitated the quantitative measurement of deregulated KLK expression in cancer, identifying certain KLKs, as well as their substrates, as potential cancer biomarkers. Areas covered: In this review, we discuss how these approaches have been utilized for KLK biomarker discovery and unbiased substrate determination in complex protein pools that mimic the in vivo extracellular microenvironment...
October 13, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#5
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29023571/pickle-2-0-a-human-protein-protein-interaction-meta-database-employing-data-integration-via-genetic-information-ontology
#6
Aris Gioutlakis, Maria I Klapa, Nicholas K Moschonas
It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets...
2017: PloS One
https://www.readbyqxmd.com/read/29022256/the-effects-of-exercise-on-cardiovascular-biomarkers-new-insights-recent-data-and-applications
#7
Lin Che, Dong Li
The benefit of regular exercise or physical activity with appropriate intensity on improving cardiopulmonary function and endurance has long been accepted with less controversy. The challenge remains, however, quantitatively evaluate the effect of exercise on cardiovascular health due in part to the amount and intensity of exercise varies widely plus lack of effective, robust and efficient biomarker evaluation systems. Better evaluating the overall function of biomarker and validate biomarkers utility in cardiovascular health should improve the evidence regarding the benefit or the effect of exercise or physical activity on cardiovascular health, in turn increasing the efficiency of the biomarker on individuals with mild to moderate cardiovascular risk...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29021832/pharmacogenomics-in-the-treatment-of-mood-disorders-strategies-and-opportunities-for-personalized-psychiatry
#8
REVIEW
Azmeraw T Amare, Klaus Oliver Schubert, Bernhard T Baune
Personalized medicine (personalized psychiatry in a specific setting) is a new model towards individualized care, in which knowledge from genomics and other omic pillars (microbiome, epigenomes, proteome, and metabolome) will be combined with clinical data to guide efforts to new drug development and targeted prescription of the existing treatment options. In this review, we summarize pharmacogenomic studies in mood disorders that may lay the foundation towards personalized psychiatry. In addition, we have discussed the possible strategies to integrate data from omic pillars as a future path to personalized psychiatry...
September 2017: EPMA Journal
https://www.readbyqxmd.com/read/29019919/proteogenomics-in-aid-of-host-pathogen-interaction-studies-a-bacterial-perspective
#9
REVIEW
Ursula Fels, Kris Gevaert, Petra Van Damme
By providing useful tools to study host-pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches...
October 11, 2017: Proteomes
https://www.readbyqxmd.com/read/29019139/elucidating-cellular-metabolism-and-protein-difference-data-from-dige-proteomics-experiments-using-enzyme-assays
#10
Andrew Dowd
Assays for measuring enzyme activity can be useful tools for proteomics applications. Enzyme testing can be performed to validate an experimental system prior to a Difference Gel Electrophoresis (DIGE) proteomic experiment and can also be utilized as an integral part of multifaceted experiment in conjunction with DIGE. Data from enzyme tests can be used to corroborate results of DIGE proteomic experiments where an enzyme or enzymes are demonstrated by DIGE to be differentially expressed. Enzyme testing can also be utilized to support data from DIGE experiments that demonstrate metabolic changes in a biological system...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29019120/two-dimensional-gel-electrophoresis-and-2d-dige
#11
Paula Meleady
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system. In particular, a modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29018800/asthma-endotypes-and-an-overview-of-targeted-therapy-for-asthma
#12
REVIEW
Sarah Svenningsen, Parameswaran Nair
Guidelines for the management of severe asthma do not emphasize the measurement of the inflammatory component of airway disease to indicate appropriate treatments or to monitor response to treatment. Inflammation is a central component of asthma and contributes to symptoms, physiological, and structural abnormalities. It can be assessed by a number of endotyping strategies based on "omics" technology such as proteomics, transcriptomics, and metabolomics. It can also be assessed using simple cellular responses by quantitative cytometry in sputum...
2017: Frontiers in Medicine
https://www.readbyqxmd.com/read/29018283/codon-optimality-bias-and-usage-in-translation-and-mrna-decay
#13
REVIEW
Gavin Hanson, Jeff Coller
The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery...
October 11, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28992342/the-endoplasmic-reticulum-is-a-hub-to-sort-proteins-toward-unconventional-traffic-pathways-and-endosymbiotic-organelles
#14
Michele Bellucci, Francesca De Marchis, Andrea Pompa
The discovery that much of the extracellular proteome in eukaryotic cells consists of proteins lacking a signal peptide, which cannot therefore enter the secretory pathway, has led to the identification of alternative protein secretion routes bypassing the Golgi apparatus. However, proteins harboring a signal peptide for translocation into the endoplasmic reticulum can also be transported along these alternative routes, which are still far from being well elucidated in terms of the molecular machineries and subcellular/intermediate compartments involved...
August 18, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28991233/dna-methylation-aberrancies-delineate-clinically-distinct-subsets-of-colorectal-cancer-and-provide-novel-targets-for-epigenetic-therapies
#15
REVIEW
D J Weisenberger, G Liang, H-J Lenz
Colorectal cancer (CRC) is a worldwide health concern with respect to both incidence and mortality, and as a result, CRC tumorigenesis, progression and metastasis have been heavily studied, especially with respect to identifying genetic, epigenetic, transcriptomic and proteomic profiles of disease. DNA methylation alterations are hallmarks of CRC, and epigenetic driver genes have been identified that are thought to be involved in early stages of tumorigenesis. Moreover, distinct CRC patient subgroups are organized based on DNA methylation profiles...
October 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28990809/proteomic-interrogation-of-hsp90-and-insights-for-medical-research
#16
Lorenz Weidenauer, Tai Wang, Suhasini Joshi, Gabriela Chiosis, Manfredo R Quadroni
Heat shock protein 90 (HSP90) regulates protein homeostasis in eukaryotes. As a "professional interactor", HSP90 binds to and chaperones many proteins and has both housekeeping and disease-related functions but its regulation remains in part elusive. HSP90 complexes are a target for therapy, notably against cancer, and several inhibitors are currently in clinical trials. Proteomic studies have revealed the vast interaction network of HSP90 and, in doing so, the extent of cellular processes the chaperone takes part in, especially in yeast and human cells...
October 9, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28988882/gender-proteomics-i-which-proteins-in-non-sexual-organs
#17
Elisabetta Gianazza, Ingrid Miller, Uliano Guerrini, Luca Palazzolo, Chiara Parravicini, Ivano Eberini
Differences related to gender have long been neglected but recent investigations show that they are widespread and may be recognized with all types of omics approaches, both in tissues and in biological fluids. Our review compiles evidence collected with proteomics techniques in our species, mainly focusing on baseline parameters in non-sexual organs in healthy men and women. Data from human specimens had to be replaced with information from other mammals every time invasive procedures of sample procurement were involved...
October 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28988880/gender-proteomics-ii-which-proteins-in-sexual-organs
#18
Elisabetta Gianazza, Ingrid Miller, Uliano Guerrini, Luca Palazzolo, Chiara Parravicini, Ivano Eberini
In continuity with the review dealing with differences by gender in non-sexual organs [1], this review collects data on the proteomes of the sexual organs as involved in human reproduction, under both physiological and pathological conditions. It also collects data on the tissue structures and biological fluids typical of pregnancy, such as placenta and amniotic fluid, as well as what may be tested on preimplantation embryos during medically assisted reproduction. The review includes as well mention to all fluids and secretions connected with sex organs and/or reproduction, including sperm and milk, to exemplify two distinctive items in male and female physiology...
October 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28988430/recent-advances-in-methods-for-the-analysis-of-protein-o-glycosylation-at-proteome-level
#19
REVIEW
Xin You, Hongqiang Qin, Mingliang Ye
O-Glycosylation, which refers to the glycosylation of the hydroxyl group of side chains of Serine/Threonine/Tyrosine residues, is one of the most common post-translational modifications. Compared with N-linked glycosylation, O-glycosylation is less explored because of its complex structure and relatively low abundance. Recently, O-glycosylation has drawn more and more attention for its various functions in many sophisticated biological processes. To obtain a deep understanding of O-glycosylation, many efforts have been devoted to develop effective strategies to analyze the two most abundant types of O-glycosylation, i...
October 8, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28984593/exploring-erythrocytes-as-blood-biomarkers-for-alzheimer-s-disease
#20
Anna Stevenson, Dianne Lopez, Paul Khoo, Rajesh N Kalaria, Elizabeta B Mukaetova-Ladinska
Peripheral biomarkers for dementia are few and far between. Despite research into blood plasma/serum biomarkers for dementia diagnostics, there is a lack of information on erythrocytes and their vast proteomes as potential biomarkers. This review identifies a number of relevant and potentially promising erythrocyte biomarkers for various subtypes of dementia. These include erythrocyte morphology, oxidative stress, and erythrocyte membrane proteins such as the glucose transporter (GLUT-1), amyloid-β, IgG, Hsp90, calpain-1, and band 3 protein...
2017: Journal of Alzheimer's Disease: JAD
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