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https://www.readbyqxmd.com/read/28534676/applications-of-raman-spectroscopy-in-biopharmaceutical-manufacturing-a-short-review
#1
Kevin Buckley, Alan G Ryder
The production of active pharmaceutical ingredients (APIs) is currently undergoing its biggest transformation in a century. The changes are based on the rapid and dramatic introduction of protein- and macromolecule-based drugs (collectively known as biopharmaceuticals) and can be traced back to the huge investment in biomedical science (in particular in genomics and proteomics) that has been ongoing since the 1970s. Biopharmaceuticals (or biologics) are manufactured using biological-expression systems (such as mammalian, bacterial, insect cells, etc...
June 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28532233/updates-on-sj%C3%A3-gren-s-syndrome-from-proteomics-to-protein-biomarkers
#2
Chiara Baldini, Antonella Cecchettini, Alessia Gallo, Stefano Bombardieri
Primary Sjögren's syndrome (pSS) is a complex heterogeneous autoimmune disorder, typically affecting exocrine glands. Recently, a great interest has arisen in searching for novel biomarkers able to improve the diagnostic work-up of the disease as well as the general assessment and the prognostic stratification of pSS patients. From this perspective, salivary proteomics has appeared as a promising tool considering that salivary proteins may closely reflect the underlying disease processes in the salivary glands...
May 23, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28532181/exploring-ribosome-composition-and-newly-synthesized-proteins-through-proteomics-and-potential-biomedical-applications
#3
Miroslava Stastna, Roberta A Gottlieb, Jennifer E Van Eyk
Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation...
May 22, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28531225/protein-charge-distribution-in-proteomes-and-its-impact-on-translation
#4
Rodrigo D Requião, Luiza Fernandes, Henrique José Araujo de Souza, Silvana Rossetto, Tatiana Domitrovic, Fernando L Palhano
As proteins are synthesized, the nascent polypeptide must pass through a negatively charged exit tunnel. During this stage, positively charged stretches can interact with the ribosome walls and slow the translation. Therefore, charged polypeptides may be important factors that affect protein expression. To determine the frequency and distribution of positively and negatively charged stretches in different proteomes, the net charge was calculated for every 30 consecutive amino acid residues, which corresponds to the length of the ribosome exit tunnel...
May 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28530547/application-of-machine-learning-approaches-for-protein-protein-interactions-prediction
#5
Mengying Zhang, Qiang Su, Yi Lu, Manman Zhao, Bing Niu
BACKGROUND: Proteomics endeavors to study the structures, functions and interactions of proteins. Information of the protein-protein interactions (PPIs) helps to improve our knowledge of the functions and the 3D structures of proteins. Thus determining the PPIs is essential for the study of the proteomics. OBJECTIVE: In this review, in order to study the application of machine learning in predicting PPI, some machine learning approaches such as support vector machine (SVM), artificial neural networks (ANNs) and random forest (RF) were selected, and the examples of its applications in PPIs were listed...
May 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28530266/comparison-of-peptide-retention-prediction-algorithm-in-reversed-phase-chromatography-comment-on-predictive-chromatography-of-peptides-and-proteins-as-a-complementary-tool-for-proteomics-by-i-a-tarasova-c-d-masselon-a-v-gorshkov-and-m-v-gorshkov-analyst-2016
#6
Oleg V Krokhin
In a recent mini-review, Tarasova et al. (Analyst, 2016, 141, 4816) compared several peptide retention prediction models for reversed-phase HPLC developed for applied proteomics. The mechanism of peptide retention in RP-HPLC is very complex. Peptide separation selectivity is affected by multiple parameters of a separation system. Consequently, proper comparison of the models requires a detailed knowledge (to provide the best match) of separation conditions used to acquire both optimization and test datasets...
May 22, 2017: Analyst
https://www.readbyqxmd.com/read/28529709/last-rolls-of-the-yoyo-assessing-the-human-canonical-protein-count
#7
REVIEW
Christopher Southan
In 2004, when the protein estimate from the finished human genome was only 24,000, the surprise was compounded as reviewed estimates fell to 19,000 by 2014. However, variability in the total canonical protein counts (i.e. excluding alternative splice forms) of open reading frames (ORFs) in different annotation portals persists. This work assesses these differences and possible causes. A 16-year analysis of Ensembl and UniProtKB/Swiss-Prot shows convergence to a protein number of ~20,000. The former had shown some yo-yoing, but both have now plateaued...
2017: F1000Research
https://www.readbyqxmd.com/read/28529348/different-stationary-phase-selectivities-and-morphologies-for-intact-protein-separations
#8
REVIEW
A Astefanei, I Dapic, M Camenzuli
The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms of their post-translational modifications, which often regulate their function within the body. Understanding the proteins within our bodies is a key step in understanding the cause, and perhaps the solution, to disease...
2017: Chromatographia
https://www.readbyqxmd.com/read/28529328/perivascular-adipose-tissue-epiphenomenon-or-local-risk-factor
#9
REVIEW
K Schäfer, I Drosos, S Konstantinides
Obesity is associated with an increased cardiovascular risk, but the mechanisms underlying the link between increased body weight and vascular disease are incompletely understood. Over the past 15 years, perivascular adipose tissue has emerged as active component of the vessel wall involved in vascular homeostasis. However, perivascular adipose tissue can adopt detrimental properties under the influence of obesity and other factors and contribute actively to the pathophysiology of cardiovascular disease. Conversely, changes of the vessel wall may negatively affect perivascular adipose tissue qualities...
May 22, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28528990/proteomics-survey-of-solanaceae-family-current-status-and-challenges-ahead
#10
Arindam Ghatak, Palak Chaturvedi, Puneet Paul, Ganesh Kumar Agrawal, Randeep Rakwal, Sun Tae Kim, Wolfram Weckwerth, Ravi Gupta
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions...
May 18, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526562/new-intracellular-activities-of-matrix-metalloproteinases-shine-in-the-moonlight
#11
REVIEW
Parker G Jobin, Georgina S Butler, ChristopherM Overall
Adaption of a single protein to perform multiple independent functions facilitates functional plasticity of the proteome allowing a limited number of protein-coding genes to perform a multitude of cellular processes. Multifunctionality is achievable by post-translational modifications and by modulating subcellular localization. Matrix metalloproteinases (MMPs), classically viewed as degraders of the extracellular matrix (ECM) responsible for matrix protein turnover, are more recently recognized as regulators of a range of extracellular bioactive molecules including chemokines, cytokines, and their binders...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28525648/the-role-of-omics-in-the-application-of-adverse-outcome-pathways-for-chemical-risk-assessment
#12
Erica K Brockmeier, Geoff Hodges, Thomas H Hutchinson, Emma Butler, Markus Hecker, Knut Erik Tollefsen, Natalia Garcia-Reyero, Peter Kille, Dörthe Becker, Kevin Chipman, John Colbourne, Timothy W Collette, Andrew Cossins, Mark Cronin, Peter Graystock, Steve Gutsell, Dries Knapen, Ioanna Katsiadaki, Anke Lange, Stuart Marshall, Stewart F Owen, Edward J Perkins, Stewart Plaistow, Anthony Schroeder, Daisy Taylor, Mark Viant, Gerald Ankley, Francesco Falciani
In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (UK) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-content omics datasets (e.g., transcriptomics, metabolomics, lipidomics, and proteomics) can hold within the adverse outcome pathway (AOP) framework for supporting ecological and human health risk assessments...
May 19, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28525563/omics-biomarkers-in-ophthalmology
#13
Susette Lauwen, Eiko K de Jong, Dirk J Lefeber, Anneke I den Hollander
"Omics" refers to high-throughput analyses of genes, proteins, or metabolites in a biological system, and is increasingly used for ophthalmic research. These system-based approaches can unravel disease-related processes and are valuable for biomarker discovery. Furthermore, potential therapeutic targets can be identified based on omics results, and targeted follow-up experiments can be designed to gain molecular understanding of the disease and to test new therapies. Here, we review the application of omics techniques in eye diseases, focusing on age-related macular degeneration (AMD), diabetic retinopathy (DR), retinal detachment (RD), myopia, glaucoma, Fuchs' corneal dystrophy (FCD), cataract, keratoconus, and dry eyes...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28523998/uncovering-drug-mechanism-of-action-by-proteome-wide-identification-of-drug-binding-proteins
#14
Tao Cui, Hai Hou, Yao Sun, Huaixing Cang, Xiangxi Wang
Small molecule drugs obtained from synthetic compounds or natural products show their therapeutic effects by specifically binding to one or a few target proteins and modulating their functions. In contrast, undesirable drug-protein interactions may provoke harmful side effects. Furthermore, drug-protein interactions also play roles in drug activation, transport, metabolism and regulation of drug resistance. Therefore, systematically identifying binding proteins of a drug molecule is critical for understanding the mechanism of action of the drug at molecular level...
May 18, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28522341/systemic-and-ocular-fluid-compounds-as-potential-biomarkers-in-age-related-macular-degeneration
#15
REVIEW
Eveline Kersten, Constantin C Paun, Rosa L Schellevis, Carel B Hoyng, Cécile Delcourt, Imre Lengyel, Tunde Peto, Marius Ueffing, Caroline C W Klaver, Sascha Dammeier, Anneke I den Hollander, Eiko K de Jong
Biomarkers can help unravel mechanisms of disease and identify new targets for therapy. They can also be useful in clinical practice for monitoring disease progression, evaluation of treatment efficacy and risk assessment in multifactorial diseases, such as age-related macular degeneration (AMD). AMD is a highly prevalent progressive retinal disorder for which multiple genetic and environmental risk factors have been described, but the exact etiology is not yet fully understood. Many compounds have been evaluated for their association with AMD...
May 15, 2017: Survey of Ophthalmology
https://www.readbyqxmd.com/read/28521948/genomics-of-interaction-between-the-brown-planthopper-and-rice
#16
REVIEW
Shengli Jing, Yan Zhao, Bo Du, Rongzhi Chen, Lili Zhu, Guangcun He
Rice (Oryza sativa L.) and the brown planthopper (Nilaparvata lugens (Stål)) form a model system for dissection of the mechanism of interaction between insect pest and crop. In this review, we focus on the genomics of BPH-rice interaction. On the side of rice, a number of BPH-resistance genes have been identified genetically. Thirteen of these genes have been cloned which shed a light on the molecular basis of the interaction. On the aspect of BPH, a lot of salivary proteins have been identified using transcriptome and proteome techniques...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28521569/exploring-the-biochemistry-of-the-prenylome-and-its-role-in-disease-through-proteomics-progress-and-potential
#17
Maura Brioschi, Alma Martinez Fernandez, Cristina Banfi
Protein prenylation is a ubiquitous covalent post-translational modification characterized by the addition of farnesyl or geranylgeranyl isoprenoid groups to a cysteine residue located near the carboxyl terminal of a protein. It is essential for the proper localization and cellular activity of numerous proteins, including Ras family GTPases and G-proteins. In addition to its roles in cellular physiology, the prenylation process has important implications in human diseases and in the recent years, it has become attractive target of inhibitors with therapeutic potential...
May 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28520864/from-chromatogram-to-analyte-to-metabolite-how-to-pick-horses-for-courses-from-the-massive-web-resources-for-mass-spectral-plant-metabolomics
#18
Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R Fernie
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell towards the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome with the number of metabolites in the plant kingdom generally being considered to be in excess of 200 000. In this review we focus on web-resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification...
May 17, 2017: GigaScience
https://www.readbyqxmd.com/read/28513226/application-of-proteomics-to-the-study-of-helicobacter-pylori-and-implications-for-the-clinic
#19
Giulia Bernardini, Natale Figura, Antonio Ponzetto, Barbara Marzocchi, Annalisa Santucci
Helicobacter pylori (H. pylori) is a gram-negative bacterium that colonizes the gastric epithelium and mucous layer of more than half the world's population. H. pylori is a primary human pathogen, responsible for the development of chronic gastritis, peptic ulceration and gastric cancer. Proteomics is impacting several aspects of medical research: understanding the molecular basis of infection and disease manifestation, identification of therapeutic targets and discovery of clinically relevant biomarkers. Areas covered: The main aim of the present review is to provide a comprehensive overview of the contribution of proteomics to the study of H...
May 17, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28512398/protein-homeostasis-in-amyotrophic-lateral-sclerosis-therapeutic-opportunities
#20
REVIEW
Christopher P Webster, Emma F Smith, Pamela J Shaw, Kurt J De Vos
Protein homeostasis (proteostasis), the correct balance between production and degradation of proteins, is essential for the health and survival of cells. Proteostasis requires an intricate network of protein quality control pathways (the proteostasis network) that work to prevent protein aggregation and maintain proteome health throughout the lifespan of the cell. Collapse of proteostasis has been implicated in the etiology of a number of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), the most common adult onset motor neuron disorder...
2017: Frontiers in Molecular Neuroscience
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