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https://www.readbyqxmd.com/read/28820493/marine-lipids-on-cardiovascular-diseases-and-other-chronic-diseases-induced-by-diet-an-insight-provided-by-proteomics-and-lipidomics
#1
REVIEW
Lucía Méndez, Gabriel Dasilva, Nùria Taltavull, Marta Romeu, Isabel Medina
Marine lipids, especially ω-3 polyunsaturated fatty acids (PUFAs) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), have largely been linked to prevention of diet-induced diseases. The anti-inflammatory and hypolipidemic properties of EPA and DHA supplementation have been well-described. However, there is still a significant lack of information about their particular mechanism of action. Furthermore, repeated meta-analyses have not shown conclusive results in support of their beneficial health effects...
August 18, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28820289/recent-advances-in-quantitative-and-chemical-proteomics-for-autophagy-studies
#2
Yin-Kwan Wong, Jianbin Zhang, Zi-Chun Hua, Qingsong Lin, Han-Ming Shen, Jigang Wang
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process...
August 18, 2017: Autophagy
https://www.readbyqxmd.com/read/28811299/twenty-years-of-menin-emerging-opportunities-for-restoration-of-transcription-in-men1
#3
Koen M A Dreijerink, Marc Timmers, Myles Brown
Since the discovery of the multiple endocrine neoplasia type 1 (MEN1) gene in 1997, elucidation of the molecular function of its protein product, menin, has been a challenge. Biochemical, proteomics, genetics and genomics approaches have identified various potential roles, which converge on gene expression regulation. The most consistent findings show that menin connects transcription factors and chromatin modifying enzymes, in particular the histone H3K4 methyltransferase complexes MLL1 and MLL2. Chromatin immunoprecipitation combined with next generation sequencing has enabled studying genome-wide dynamics of chromatin binding by menin...
August 15, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28810194/towards-detecting-regulatory-protein-metabolite-interactions
#4
REVIEW
Maren Diether, Uwe Sauer
New mapping approaches have greatly expanded our view on the cellular landscape of protein-metabolite interactions. These methods either identify proteins interacting with a selected metabolite or vice versa. By reviewing recent developments, we found that comprehensive mapping of the protein-metabolite interaction space can be achieved eventually using existing methods, amongst which proteomics techniques to assess cell wide protein property changes in response to metabolite treatment currently offer the highest potential...
August 12, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28808043/allosteric-alterations-in-the-androgen-receptor-and-activity-in-prostate-cancer
#5
REVIEW
Takuma Uo, Stephen R Plymate, Cynthia C Sprenger
Organisms have evolved to generate biological complexity in their proteome and transcriptome from a limited number of genes. This concept holds true for the androgen receptor, which displays a diversity of inclusion/exclusion events in its structural motifs as a mechanism of resistance to the most forefront anti-androgen therapies. More than 20 androgen receptor variants that lack various portions of ligand-binding domain have been identified in human prostate cancer (PCa) samples. Most of the variants are inactive on their own, with a few exceptions displaying constitutive activity...
September 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28807817/assessment-of-glutathione-glutathione-disulphide-ratio-and-s-glutathionylated-proteins-in-human-blood-solid-tissues-and-cultured-cells
#6
REVIEW
Daniela Giustarini, Graziano Colombo, Maria Lisa Garavaglia, Emanuela Astori, Nicola Marcello Portinaro, Francesco Reggiani, Salvatore Badalamenti, Anna Maria Aloisi, Annalisa Santucci, Ranieri Rossi, Aldo Milzani, Isabella Dalle-Donne
Glutathione (GSH) is the major non-protein thiol in humans and other mammals, which is present in millimolar concentrations within cells, but at much lower concentrations in the blood plasma. GSH and GSH-related enzymes act both to prevent oxidative damage and to detoxify electrophiles. Under oxidative stress, two GSH molecules become linked by a disulphide bridge to form glutathione disulphide (GSSG). Therefore, assessment of the GSH/GSSG ratio may provide an estimation of cellular redox metabolism. Current evidence resulting from studies in human blood, solid tissues, and cultured cells suggests that GSH also plays a prominent role in protein redox regulation via S-glutathionylation, i...
August 11, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28807694/reviewing-evidence-for-systematic-transcriptional-deletions-nucleotide-exchanges-and-expanded-codons-and-peptide-clusters-in-human-mitochondria
#7
REVIEW
Hervé Seligmann
Polymerization sometimes transforms sequences by (a) systematic deletions of mono-, dinucleotides after trinucleotides, or (b) 23 systematic nucleotide exchanges (9 symmetric, X<>Y, e.g. G<>T, 14 asymmetric, X > Y > Z > X, e.g. A > G > T > A), producing del- and swinger RNAs. Some peptides correspond to del- and swinger RNA translations, also according to tetracodons, codons expanded by a silent nucleotide. Here new analyzes assume different proteolytic patterns, partially alleviating false negative peptide detection biases, expanding noncanonical mitoproteome profiles...
August 11, 2017: Bio Systems
https://www.readbyqxmd.com/read/28806595/advances-in-stem-cell-proteomics
#8
REVIEW
Nade Abazova, Jeroen Krijgsveld
Stem cells are at the basis of organismal development, characterized by their potential to differentiate towards specific lineages upon receiving proper signals. To understand the molecular principles underlying gain and loss of pluripotency, proteomics plays an increasingly important role owing to technical developments in mass spectrometry and implementation of innovative biochemical approaches. Here we review how quantitative proteomics has been used to investigate protein expression, localization, interaction and modification in stem cells both in vitro and in vivo, thereby complementing other omics approaches to study fundamental properties of stem cell plasticity...
August 11, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28802714/in-silico-structure-based-approaches-to-discover-protein-protein-interaction-targeting-drugs
#9
REVIEW
Woong-Hee Shin, Charles W Christoffer, Daisuke Kihara
A core concept behind modern drug discovery is finding a small molecule that modulates a function of a target protein. This concept has been successfully applied since the mid-1970s. However, the efficiency of drug discovery is decreasing because the druggable target space in the human proteome is limited. Recently, protein-protein interaction (PPI) has been identified as an emerging target space for drug discovery. PPI plays a pivotal role in biological pathways including diseases. Current human interactome research suggests that the number of PPIs ranges from 130,000 to 650,000, and only a small number of them have been targeted as drug targets...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28802010/quality-control-in-mass-spectrometry-based-proteomics
#10
REVIEW
Wout Bittremieux, David L Tabb, Francis Impens, An Staes, Evy Timmerman, Lennart Martens, Kris Laukens
Mass spectrometry is a highly complex analytical technique and mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining accurate and reproducible results. Therefore, a comprehensive and systematic approach to quality control is an essential requirement to inspire confidence in the generated results. A typical mass spectrometry experiment consists of multiple different phases including the sample preparation, liquid chromatography, mass spectrometry, and bioinformatics stages...
August 12, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28799854/proteomic-studies-in-the-discovery-of-cerebrospinal-fluid-biomarkers-for-amyotrophic-lateral-sclerosis
#11
Peggy Barschke, Patrick Oeckl, Petra Steinacker, Albert Ludolph, Markus Otto
Amyotrophic lateral sclerosis (ALS) is a progressive degenerative motor neuron disease, which usually leads to death within a few years. The diagnosis is mainly based on clinical symptoms and there is a need for ALS-specific biomarkers to make an early and precise diagnosis, for development of disease-modifying drugs and to gain new insights into pathophysiology. Areas covered: In the present review, we summarize studies using mass spectrometric (MS) approaches to identify protein alterations in the cerebrospinal fluid (CSF) of ALS patients...
August 14, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28798504/molecular-aspects-of-wound-healing-and-the-rise-of-venous-leg-ulceration-omics-approaches-to-enhance-knowledge-and-aid-diagnostic-discovery
#12
REVIEW
Daniel A Broszczak, Elizabeth R Sydes, Daniel Wallace, Tony J Parker
Chronic wounds, in particular venous leg ulcers (VLU), represent a substantial burden for economies, healthcare systems and societies worldwide. This burden is exacerbated by the recalcitrant nature of these wounds, despite best practice, evidence-based care, which substantially reduces the quality of life of patients. Furthermore, co-morbidities such as diabetes and cardiovascular disease within ageing populations further contribute to the increasing prevalence in developed countries. This review provides an overview of the literature concerning the cellular and molecular mechanisms of wound healing and aspects where this process fails, resulting in a chronic wound...
February 2017: Clinical Biochemist. Reviews
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#13
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features...
August 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28794464/expression-changes-in-pelvic-organ-prolapse-a-systematic-review-and-in-silico-study
#14
Maryam B Khadzhieva, Dmitry S Kolobkov, Svetlana V Kamoeva, Lyubov E Salnikova
Pelvic organ prolapse (POP) is a highly disabling condition common for a vast number of women worldwide. To contribute to existing knowledge in POP pathogenesis, we performed a systematic review of expression studies on both specific gene and whole-genome/proteome levels and an in silico analysis of publicly available datasets related to POP development. The most extensively investigated genes in individual studies were related to extracellular matrix (ECM) organization. Three premenopausal and two postmenopausal sets from two Gene Expression Omnibus (GEO) studies (GSE53868 and GSE12852) were analyzed; Gene Ontology (GO) terms related to tissue repair (locomotion, biological adhesion, immune processes and other) were enriched in all five datasets...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28789751/biological-markers-in-nursing-research
#15
Sheila A Alexander, Karen Kalmakis, Pamela S Stewart Fahs, Susan W Groth, Eileen R Chasens
INTRODUCTION: Biobehavioral research requires the ability to objectively measure the presence and/or severity of disease, symptoms and their burden, or to determine the effect of treatment on outcomes. Biomarker research has advanced care for patients across the lifespan. There have been significant advancements in biological marker use for nursing research in recent years. The purposes of this article are to define the characteristics of a valid biomarker; review common biological sources of genetic, hormonal, and proteomic biomarkers with attention to practical strengths, weaknesses, and challenges for specimen selection and quality; and discuss potential use of biomarkers in clinical and research settings...
August 1, 2017: Journal of Nursing Measurement
https://www.readbyqxmd.com/read/28783379/phenotypic-and-genetic-heterogeneity-within-biofilms-with-particular-emphasis-on-persistence-and-antimicrobial-tolerance
#16
Faizan A Sadiq, Steve Flint, YanJun Li, Kai Ou, Lei Yuan, Guo Qing He
Phenotypic changes or phase variation within biofilms is an important feature of bacterial dormant life. Enhanced resistance to antimicrobials is one of the distinct features displayed by a fraction of cells within biofilms. It is believed that persisters are mainly responsible for this phenotypic heterogeneity. However, there is still an unresolved debate on the formation of persisters. In this short review, we highlight all known genomic and proteomic changes encountered by bacterial cells within biofilms...
August 7, 2017: Future Microbiology
https://www.readbyqxmd.com/read/28783113/-omics-in-human-colostrum-and-mature-milk-looking-to-old-data-with-new-eyes
#17
REVIEW
Flaminia Bardanzellu, Vassilios Fanos, Alessandra Reali
Human Milk (HM) is the best source for newborn nutrition until at least six months; it exerts anti-inflammatory and anti-infective functions, promotes immune system formation and supports organ development. Breastfeeding could also protect from obesity, diabetes and cardiovascular disease. Furthermore, human colostrum (HC) presents a peculiar role in newborn support as a protective effect against allergic and chronic diseases, in addition to long-term metabolic benefits. In this review, we discuss the recent literature regarding "omics" technologies and growth factors (GF) in HC and the effects of pasteurization on its composition...
August 7, 2017: Nutrients
https://www.readbyqxmd.com/read/28782657/the-search-for-novel-diagnostic-and-prognostic-biomarkers-in-cholangiocarcinoma
#18
REVIEW
Rocio I R Macias, Jesus M Banales, Bruno Sangro, Jordi Muntané, Matias A Avila, Elisa Lozano, Maria J Perugorria, Francisco J Padillo, Luis Bujanda, Jose J G Marin
The poor prognosis of cholangiocarcinoma (CCA) is in part due to late diagnosis, which is currently achieved by a combination of clinical, radiological and histological approaches. Available biomarkers determined in serum and biopsy samples to assist in CCA diagnosis are not sufficiently sensitive and specific. Therefore, the identification of new biomarkers, preferably those obtained by minimally invasive methods, such as liquid biopsy, is important. The development of innovative technologies has permitted to identify a significant number of genetic, epigenetic, proteomic and metabolomic CCA features with potential clinical usefulness in early diagnosis, prognosis or prediction of treatment response...
August 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28780899/mapping-the-human-skeletal-muscle-proteome-progress-and-potential
#19
Daniele Capitanio, Manuela Moriggi, Cecilia Gelfi
Abtract Introduction: Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies...
August 7, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28777303/novel-biomarkers-in-the-diagnosis-of-chronic-kidney-disease-and-the-prediction-of-its-outcome
#20
REVIEW
Jacek Rysz, Anna Gluba-Brzózka, Beata Franczyk, Zbigniew Jabłonowski, Aleksandra Ciałkowska-Rysz
In its early stages, symptoms of chronic kidney disease (CKD) are usually not apparent. Significant reduction of the kidney function is the first obvious sign of disease. If diagnosed early (stages 1 to 3), the progression of CKD can be altered and complications reduced. In stages 4 and 5 extensive kidney damage is observed, which usually results in end-stage renal failure. Currently, the diagnosis of CKD is made usually on the levels of blood urea and serum creatinine (sCr), however, sCr has been shown to be lacking high predictive value...
August 4, 2017: International Journal of Molecular Sciences
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