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https://www.readbyqxmd.com/read/28934504/accumulation-of-histone-variant-h3-3-with-age-is-associated-with-profound-changes-in-the-histone-methylation-landscape
#1
Andrey Tvardovskiy, Veit Schwämmle, Stefan J Kempf, Adelina Rogowska-Wrzesinska, Ole N Jensen
Deposition of replication-independent histone variant H3.3 into chromatin is essential for many biological processes, including development and reproduction. Unlike replication-dependent H3.1/2 isoforms, H3.3 is expressed throughout the cell cycle and becomes enriched in postmitotic cells with age. However, lifelong dynamics of H3 variant replacement and the impact of this process on chromatin organization remain largely undefined. Using quantitative middle-down proteomics we demonstrate that H3.3 accumulates to near saturation levels in the chromatin of various mouse somatic tissues by late adulthood...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933646/visualizing-trna-dependent-mistranslation-in-human-cells
#2
Jeremy T Lant, Matthew D Berg, Daniel Hw Sze, Kyle S Hoffman, Ibukunoluwa C Akinpelu, Matthew Turk, Ilka U Heinemann, Martin L Duennwald, Christopher J Brandl, Patrick O'Donoghue
High-fidelity translation and a strictly accurate proteome were originally assumed as essential to life and cellular viability. Yet recent studies in bacteria and eukaryotic model organisms suggest that proteome-wide mistranslation can provide selective advantages and is tolerated in the cell at higher levels than previously thought (one error in 6.9 × 10(-4) in yeast) with a limited impact on phenotype. Previously, we selected a tRNA(Pro) containing a single mutation that induces mistranslation with alanine at proline codons in yeast...
September 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28933642/epitope-characterization-of-anti-jam-a-antibodies-using-orthogonal-mass-spectrometry-and-surface-plasmon-resonance-approaches
#3
Guillaume Terral, Thierry Champion, François Debaene, Olivier Colas, Maxime Bourguet, Elsa Wagner-Rousset, Nathalie Corvaia, Alain Beck, Sarah Cianferani
Junctional adhesion molecule-A (JAM-A) is an adherens and tight junction protein expressed by endothelial and epithelial cells and associated with cancer progression. We present here the extensive characterization of immune complexes involving JAM-A antigen and three monoclonal antibodies (mAbs), including hz6F4-2, a humanized version of anti-tumoral 6F4 mAb identified by a functional and proteomic approach in our laboratory. A specific workflow that combines orthogonal approaches has been designed to determine binding stoichiometries along with JAM-A epitope mapping determination at high resolution for these three mAbs...
September 21, 2017: MAbs
https://www.readbyqxmd.com/read/28933156/we-are-not-alone-the-imop-initiative-and-its-roles-in-a-biology-and-disease-driven-human-proteome-project
#4
Andreas Tholey, Nicolas L Taylor, Joshua L Heazlewood, Emøke Bendixen
The Human Proteome is nearly fully mapped and will provide a knowledge base to accelerate our understanding of how proteins and protein networks can affect human health and disease. However, providing solutions to human health challenges will likely fail if insights are exclusively based on studies of human samples and human proteomes. In recent years, it has become evident that human health depends on an integrated understanding of the many species that make human life possible. These include the commensal microorganisms which are essential to human life, pathogens and food species as well as the classic model organisms that enable studies of biological mechanisms...
September 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28932706/global-proteomics-revealed-klebsiella-pneumoniae-induced-autophagy-and-oxidative-stress-in-caenorhabditis-elegans-by-inhibiting-pi3k-akt-mtor-pathway-during-infection
#5
Arumugam Kamaladevi, Krishnaswamy Balamurugan
The enterobacterium, Klebsiella pneumoniae invades the intestinal epithelium of humans by interfering with multiple host cell response. To uncover a system-level overview of host response during infection, we analyzed the global dynamics of protein profiling in Caenorhabditis elegans using quantitative proteomics approach. Comparison of protein samples of nematodes exposed to K. pneumoniae for 12, 24, and 36 h by 2DE revealed several changes in host proteome. A total of 266 host-encoded proteins were identified by 2DE MALDI-MS/MS and LC-MS/MS and the interacting partners of the identified proteins were predicted by STRING 10...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28932152/human-salivary-protein-extraction-from-rnapro%C3%A2-sal%C3%A2-pure%C3%A2-sal%C3%A2-and-passive-drooling-method
#6
Zohaib Khurshid, Syed Faraz Moin, Rabia Sannam Khan, Muhammad Atif Saleem Agwan, Abdullah Hamed Alwadaani, Muhammad Sohail Zafar
OBJECTIVE: The aim of the current study was to carry out a preliminary validation of devices for standardized collection of whole mouth fluid (WMF) in comparison to the passive drooling method for protein analysis in healthy subjects. MATERIALS AND METHODS: A carefully designed sample collection/pretreatment protocol is crucial to the success of any saliva proteomics project. In this study, WMF was collected from healthy volunteers (n = 10, ages: 18-26 years). Individuals with any oral disease were excluded from the study group...
July 2017: European Journal of Dentistry
https://www.readbyqxmd.com/read/28930429/mapping-protein-targets-of-bioactive-small-molecules-using-lipid-based-chemical-proteomics
#7
Kenneth M Lum, Yoshiaki Sato, Brittney A Beyer, Warren C Plaisted, Justin L Anglin, Luke L Lairson, Benjamin F Cravatt
Lipids play critical roles in cell biology, often through direct interactions with proteins. We recently described the use of photoreactive lipid probes combined with quantitative mass spectrometry to globally map lipid-protein interactions, and the effects of drugs on these interactions, in cells. Here, we investigate the broader potential of lipid-based chemical proteomic probes for determining the cellular targets of biologically active small molecules, including natural product derivatives and repurposed drugs of ill-defined mechanisms...
September 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28929768/protein-corona-analysis-of-silver-nanoparticles-links-to-their-cellular-effects
#8
Sabine Juling, Alicia Niedzwiecka, Linda Böhmert, Dajana Lichtenstein, Soeren Selve, Albert Braeuning, Andreas F Thünemann, Eberhard Krause, Alfonso Lampen
The breadth of applications of nanoparticles and the access to food-associated consumer products containing nano-sized materials lead to oral human exposure to such particles. In biological fluids nanoparticles dynamically interact with biomolecules and form a protein corona. Knowledge about the protein corona is of great interest for understanding the molecular effects of particles as well as their fate inside the human body. We used a mass spectrometry-based toxicoproteomics approach to elucidate mechanisms of toxicity of silver nanoparticles and to comprehensively characterize the protein corona formed around silver nanoparticles in Caco-2 human intestinal epithelial cells...
September 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28929764/decoding-the-effect-of-isobaric-substitutions-on-identifying-missing-proteins-and-variant-peptides-in-human-proteome
#9
Wai-Kok Choong, Tung-Shing Mamie Lih, Yu-Ju Chen, Ting-Yi Sung
To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9-40 amino acids of a missing protein in bottom-up mass spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobaric substitutions, mass modifications, alternative splice isoforms, or single amino acid variants (SAAVs). Besides unique peptides of missing proteins, identified variant peptides (SAAV-containing peptides) could also alternatively map to peptides of other proteins due to the aforementioned issues...
September 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#10
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28928079/polyglutamine-expansion-diseases-more-than-simple-repeats
#11
Alexandra Silva, Ana Viana de Almeida, Sandra Macedo-Ribeiro
Polyglutamine (polyQ) repeat-containing proteins are widespread in the human proteome but only nine of them are associated with highly incapacitating neurodegenerative disorders. The genetic expansion of the polyQ tract in disease-related proteins triggers a series of events resulting in neurodegeneration. The polyQ tract plays the leading role in the aggregation mechanism, but other elements modulate the aggregation propensity in the context of the full-length proteins, as implied by variations in the length of the polyQ tract required to trigger the onset of a given polyQ disease...
September 16, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28927277/benchmark-dose-modeling-estimates-of-the-concentrations-of-inorganic-arsenic-that-induce-changes-to-the-neonatal-transcriptome-proteome-and-epigenome-in-a-pregnancy-cohort
#12
Julia Rager, Scott S Auerbach, Grace A Chappell, Elizabeth Martin, Chad Thompson, Rebecca C Fry
Prenatal inorganic arsenic (iAs) exposure influences the expression of critical genes and proteins associated with adverse outcomes in newborns, in part through epigenetic mediators. The doses at which these genomic and epigenomic changes occur have yet to be evaluated in the context of dose-response modeling. The goal of the present study was to estimate iAs doses that correspond to changes in transcriptomic, proteomic, epigenomic, and integrated multi-omic signatures in human cord blood through benchmark dose (BMD) modeling...
September 19, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28926938/integrin-activation-contributes-to-lower-cisplatin-sensitivity-in-mv3-melanoma-cells-by-inducing-the-wnt-signalling-pathway
#13
Maria B R Piva, Bastian Jakubzig, Gerd Bendas
BACKGROUND: integrins have been associated with the development of chemotherapy resistant tumour cells, mostly those of hematopoietic origin, by mediating the binding to the extracellular matrix. The relevance for solid tumour cells and the underlying mechanisms remain elusive. METHODS: using MTT assays, we detected the loss in cisplatin sensitivity of human MV3 melanoma cells upon integrin activation. Underlying cellular pathways were evaluated by flow cytometry...
September 16, 2017: Cancers
https://www.readbyqxmd.com/read/28924605/pai-1-is-a-critical-regulator-of-fgf23-homeostasis
#14
Mesut Eren, Aaron T Place, Paul M Thomas, Panagiotis Flevaris, Toshio Miyata, Douglas E Vaughan
Elevated levels of fibroblast growth factor 23 (FGF23), a bone-derived phosphaturic hormone, are associated with a number of pathologic conditions including chronic kidney disease, cardiac hypertrophy, and congestive heart failure. Currently, there are no specific treatments available to lower plasma FGF23 levels. We have recently reported that genetic plasminogen activator inhibitor-1 (PAI-1) deficiency provided a significant reduction in circulating FGF23 levels while simultaneously prolonging the life span of Klotho-deficient mice...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28924191/metabolic-crosstalk-regulates-porphyromonas-gingivalis-colonization-and-virulence-during-oral-polymicrobial-infection
#15
Masae Kuboniwa, John R Houser, Erik L Hendrickson, Qian Wang, Samar A Alghamdi, Akito Sakanaka, Daniel P Miller, Justin A Hutcherson, Tiansong Wang, David A C Beck, Marvin Whiteley, Atsuo Amano, Huizhi Wang, Edward M Marcotte, Murray Hackett, Richard J Lamont
Many human infections are polymicrobial in origin, and interactions among community inhabitants shape colonization patterns and pathogenic potential (1) . Periodontitis, which is the sixth most prevalent infectious disease worldwide (2) , ensues from the action of dysbiotic polymicrobial communities (3) . The keystone pathogen Porphyromonas gingivalis and the accessory pathogen Streptococcus gordonii interact to form communities in vitro and exhibit increased fitness in vivo (3,4) . The mechanistic basis of this polymicrobial synergy, however, has not been fully elucidated...
September 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28923896/experimental-and-theoretical-approaches-to-investigate-the-immunogenicity-of-taenia-solium-derived-ke7-antigen
#16
Raúl J Bobes, José Navarrete-Perea, Adrián Ochoa-Leyva, Víctor Hugo Anaya, Marisela Hernández, Jacquelynne Cervantes-Torres, Karel Estrada, Filiberto Sánchez-Lopez, Xavier Soberón, Gabriela Rosas, Cáris Maroni Nunes, Martín García-Varela, Rogerio Rafael Sotelo-Mundo, Alonso Alexis López-Zavala, Goar Gevorkian, Gonzalo Acero, Juan P Laclette, Gladis Fragoso, Edda Sciutto
Taenia solium cysticercosis, a parasitic disease that affects human health in various regions of the world, is preventable by vaccination. Both the 97-amino-acid-long KETc7 peptide and its carboxyl-terminal, 18-amino-acid-long sequence (GK-1) are found in Taenia crassiceps Both peptides, with proven protective capacity against cysticercosis, are part of the highly conserved, cestode-native, 264-amino-acid long protein KE7. KE7 belongs to a ubiquitously distributed family of proteins associated to membrane processes and may participate in several vital cell pathways...
September 18, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#17
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28922472/mirna-506-promotes-primary-biliary-cholangitis-like-features-in-cholangiocytes-and-immune-activation
#18
Oihane Erice, Patricia Munoz-Garrido, Javier Vaquero, Maria J Perugorria, Maite G Fernandez-Barrena, Elena Saez, Alvaro Santos-Laso, Ander Arbelaiz, Raul Jimenez-Agüero, Joaquin Fernandez-Irigoyen, Enrique Santamaria, Verónica Torrano, Arkaitz Carracedo, Meenakshisundaram Ananthanarayanan, Marco Marzioni, Jesus Prieto, Ulrich Beuers, Ronald P Oude Elferink, Nicholas F LaRusso, Luis Bujanda, Jose J G Marin, Jesus M Banales
Primary biliary cholangitis (PBC) is a chronic cholestatic liver disease associated with autoimmune phenomena targeting intrahepatic bile duct cells (cholangiocytes). Although PBC etiopathogenesis still remains obscure, development of anti-mitochondrial auto-antibodies against pyruvate dehydrogenase complex-E2 (PDC-E2) is a common feature. MicroRNA (miR) dysregulation occurs in liver and immune cells of PBC patients, but their functional relevance is largely unknown. We previously reported that miR-506 is overexpressed in PBC cholangiocytes and directly targets both Cl(-) /HCO3(-) anion exchanger 2 (AE2) and type III inositol 1,4,5-trisphosphate receptor (InsP3R3), leading to cholestasis...
September 18, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28921918/proteomic-response-of-human-umbilical-vein-endothelial-cells-to-histamine-stimulation
#19
Pelin Esma Emirbayer, Ankit Sinha, Vladimir Ignatchenko, Stefanie Hoyer, Jan Dörrie, Niels Schaft, Monika Pischetsrieder, Thomas Kislinger
The histamine receptors (HRs) represent a subclass of G protein-coupled receptors (GPCRs) and comprise four subtypes. Due to their numerous physiological and pathological effects, HRs are popular drug targets for the treatment of allergic reactions or the regulation of gastric acid secretion. Hence, an understanding of the functional selectivity of HR ligands has gained importance. These ligands can bind to specific GPCRs and selectively activate defined pathways. Supporting the activation of a therapeutically necessary pathway without the activation of other signaling cascades can result in drugs with more specific activity and fewer side effects...
September 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28921609/biomarkers-for-equine-joint-injury-and-osteoarthritis
#20
REVIEW
C Wayne McIlwraith, Christopher E Kawcak, David D Frisbie, Christopher B Little, Peter D Clegg, Mandy J Peffers, Morten A Karsdal, Stina Ekman, Sheila Laverty, Richard A Slayden, Linda J Sandell, L Stefan Lohmander, Virginia B Kraus
We report the results of a symposium aimed at identifying validated biomarkers that can be used to complement clinical observations for diagnosis and prognosis of joint injury leading to equine osteoarthritis (OA). Biomarkers might also predict pre-fracture change that could lead to catastrophic bone failure in equine athletes. The workshop was attended by leading scientists in the fields of equine and human musculoskeletal biomarkers to enable cross-disciplinary exchange and improve knowledge in both. Detailed proceedings with strategic planning was written, added to, edited and referenced to develop this manuscript...
September 16, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
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