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https://www.readbyqxmd.com/read/28930429/mapping-protein-targets-of-bioactive-small-molecules-using-lipid-based-chemical-proteomics
#1
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/28923343/association-among-total-serum-isomers-of-perfluorinated-chemicals-glucose-homeostasis-lipid-profiles-serum-protein-and-metabolic-syndrome-in-adults-nhanes-2013-2014
#2
Hui-Shan Liu, Li-Li Wen, Pei-Lun Chu, Chien-Yu Lin
Perfluorinated chemicals (PFCs) have been used widely in consumer products manufacture. Recent in vitro as well as animal studies have found that there are different toxicity and pharmacokinetic profiles between isomers of perfluorooctanoic acid (PFOA) and/or perfluorooctane sulfonate (PFOS). However, the differential effects of linear or branched PFOA/PFOS isomers on human beings have never been reported. Herein, we examined 1871 adult subjects (age older than 18 years) from the National Health and Nutrition Examination Survey (NHANES) 2013-2014 to determine the association between the isomers of PFOA/PFOS and serum biochemistry profiles, including glucose, lipids, protein and components of metabolic syndrome (MS)...
September 15, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28910412/transcriptional-responses-in-the-hepatopancreas-of-eriocheir-sinensis-exposed-to-deltamethrin
#3
Zongying Yang, Yiliu Zhang, Yingying Jiang, Fengjiao Zhu, Liugen Zeng, Yulan Wang, Xiaoqing Lei, Yi Yao, Yujie Hou, Liangqing Xu, Chunxian Xiong, Xianle Yang, Kun Hu
Deltamethrin is an important pesticide widely used against ectoparasites. Deltamethrin contamination has resulted in a threat to the healthy breeding of the Chinese mitten crab, Eriocheir sinensis. In this study, we investigated transcriptional responses in the hepatopancreas of E. sinensis exposed to deltamethrin. We obtained 99,087,448, 89,086,478, and 100,117,958 raw sequence reads from control 1, control 2, and control 3 groups, and 92,094,972, 92,883,894, and 92,500,828 raw sequence reads from test 1, test 2, and test 3 groups, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28902016/raman-microscopy-a-noninvasive-method-to-visualize-the-localizations-of-biomolecules-in-the-cornea
#4
Yuichi Kaji, Toshihiro Akiyama, Hiroki Segawa, Tetsuro Oshika, Hideaki Kano
PURPOSE: In vivo and in situ visualization of biomolecules without pretreatment will be important for diagnosis and treatment of ocular disorders in the future. Recently, multiphoton microscopy, based on the nonlinear interactions between molecules and photons, has been applied to reveal the localizations of various molecules in tissues. We aimed to use multimodal multiphoton microscopy to visualize the localizations of specific biomolecules in rat corneas. METHODS: Multiphoton images of the corneas were obtained from nonlinear signals of coherent anti-Stokes Raman scattering, third-order sum frequency generation, and second-harmonic generation...
September 7, 2017: Cornea
https://www.readbyqxmd.com/read/28868334/loading-of-extracellular-vesicles-with-chemically-stabilized-hydrophobic-sirnas-for-the-treatment-of-disease-in-the-central-nervous-system
#5
Reka A Haraszti, Andrew Coles, Neil Aronin, Anastasia Khvorova, Marie-Cécile Didiot
Efficient delivery of oligonucleotide therapeutics, i.e., siRNAs, to the central nervous system represents a significant barrier to their clinical advancement for the treatment of neurological disorders. Small, endogenous extracellular vesicles were shown to be able to transport lipids, proteins and RNA between cells, including neurons. This natural trafficking ability gives extracellular vesicles the potential to be used as delivery vehicles for oligonucleotides, i.e., siRNAs. However, robust and scalable methods for loading of extracellular vesicles with oligonucleotide cargo are lacking...
June 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28862654/antioxidant-therapeutic-strategies-for-cardiovascular-conditions-associated-with-oxidative-stress
#6
REVIEW
Jorge G Farías, Víctor M Molina, Rodrigo A Carrasco, Andrea B Zepeda, Elías Figueroa, Pablo Letelier, Rodrigo L Castillo
Oxidative stress (OS) refers to the imbalance between the generation of reactive oxygen species (ROS) and the ability to scavenge these ROS by endogenous antioxidant systems, where ROS overwhelms the antioxidant capacity. Excessive presence of ROS results in irreversible damage to cell membranes, DNA, and other cellular structures by oxidizing lipids, proteins, and nucleic acids. Oxidative stress plays a crucial role in the pathogenesis of cardiovascular diseases related to hypoxia, cardiotoxicity and ischemia-reperfusion...
September 1, 2017: Nutrients
https://www.readbyqxmd.com/read/28856701/extracellular-vesicles-for-personalized-therapy-decision-support-in-advanced-metastatic-cancers-and-its-potential-impact-for-prostate-cancer
#7
REVIEW
Carolina Soekmadji, Niall M Corcoran, Irina Oleinikova, Lidija Jovanovic, Grant A Ramm, Colleen C Nelson, Guido Jenster, Pamela J Russell
The use of circulating tumor cells (CTCs) and circulating extracellular vesicles (EVs), such as exosomes, as liquid biopsy-derived biomarkers for cancers have been investigated. CTC enumeration using the CellSearch based platform provides an accurate insight on overall survival where higher CTC counts indicate poor prognosis for patients with advanced metastatic cancer. EVs provide information based on their lipid, protein, and nucleic acid content and can be isolated from biofluids and analyzed from a relatively small volume, providing a routine and non-invasive modality to monitor disease progression...
October 2017: Prostate
https://www.readbyqxmd.com/read/28852989/biophysical-aspects-of-biomineralization
#8
REVIEW
Maytê Bolean, Ana M S Simão, Marina B Barioni, Bruno Z Favarin, Heitor G Sebinelli, Ekeveliny A Veschi, Tatiane A B Janku, Massimo Bottini, Marc F Hoylaerts, Rosangela Itri, José L Millán, Pietro Ciancaglini
During the process of endochondral bone formation, chondrocytes and osteoblasts mineralize their extracellular matrix (ECM) by promoting the synthesis of hydroxyapatite (HA) seed crystals in the sheltered interior of membrane-limited matrix vesicles (MVs). Several lipid and proteins present in the membrane of the MVs mediate the interactions of MVs with the ECM and regulate the initial mineral deposition and posterior propagation. Among the proteins of MV membranes, ion transporters control the availability of phosphate and calcium needed for initial HA deposition...
August 29, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28851587/exploration-of-variations-in-proteome-and-metabolome-for-predictive-diagnostics-and-personalized-treatment-algorithms-innovative-approach-and-examples-for-potential-clinical-application
#9
Xianquan Zhan, Ying Long, Miaolong Lu
Genome mutually interacts with internal and external environmental factors to result in different phenome that contains two important elements of proteins and metabolites, which link genome to predictive, preventive and personalized medicine (PPPM) or precision medicine (PM). Proteomic variations are the final presentation of the genomic and transcriptomic variations, and are involved in a wide range of variations including copy number of protein, splicing, post-translational modifications, translocation/re-distribution, spatial conformation, and pathway-network systems...
August 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28842806/material-utilization-of-organic-residues
#10
REVIEW
Jan Christoph Peinemann, Daniel Pleissner
Each year, 1.3 billion tons of food waste is generated globally. This waste traces back to industrial and agricultural producers, bakeries, restaurants, and households. Furthermore, lignocellulosic materials, including grass clippings, leaves, bushes, shrubs, and woods, appear in large amounts. Depending on the region, organic waste is either composted, burned directly, or converted into biogas. All of the options set aside the fact that organic residues are valuable resources containing carbohydrates, lipids, proteins, and phosphorus...
August 25, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28833502/tumor-derived-exosomes-potential-biomarker-or-therapeutic-target-in-breast-cancer
#11
AmirReza Hesari, Seyed Ali Golrokh Moghadam, AmirShayan Siasi, Mahsa Rahmani, Negin Behboodi, Azam Rastgar-Moghadam, Gordon A Ferns, Faezeh Ghasemi, Amir Avan
Exosomes are released by normal and tumour cells, including those involved in breast cancer, and provide a means of intercellular communications. Exosomes with diameters ranging between 30-150 nm are involved in transferring biological information, via various lipids, proteins, different forms of RNAs, and DNA from one cell to another, and this can result in reprogramming of recipient cell functions. These vesicles are present in all body fluids, e.g., blood plasma/serum, semen, saliva, cerebrospinal fluid, breast milk, and urine...
August 18, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28832692/microfluidics-for-exosome-isolation-and-analysis-enabling-liquid-biopsy-for-personalized-medicine
#12
REVIEW
Jose C Contreras-Naranjo, Hung-Jen Wu, Victor M Ugaz
Exosomes, the smallest sized extracellular vesicles (∽30-150 nm) packaged with lipids, proteins, functional messenger RNAs and microRNAs, and double-stranded DNA from their cells of origin, have emerged as key players in intercellular communication. Their presence in bodily fluids, where they protect their cargo from degradation, makes them attractive candidates for clinical application as innovative diagnostic and therapeutic tools. But routine isolation and analysis of high purity exosomes in clinical settings is challenging, with conventional methods facing a number of drawbacks including low yield and/or purity, long processing times, high cost, and difficulties in standardization...
August 23, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28828667/an-adaptable-polyethylene-glycol-based-workflow-for-proteomic-analysis-of-extracellar-vesicles
#13
Stephanie N Hurwitz, David G Meckes
Extracellular vesicles (EVs), including exosomes are endocytically derived nanovesicles expelled from cells that contain molecular information in the form of lipids, proteins, and nucleic acids. Transfer of this information to other cells in local or distant microenvironments facilitates cell-to-cell communication. Importantly, diseased cells release exosomes containing specific cargo that may contribute to pathology and can be harnessed for diagnostic or prognostic use. The broad potential medical utility of exosomes has fueled rapidly expanding research on understanding the composition and functions of exosomes in normal and pathological conditions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28804598/a-rigorous-method-to-enrich-for-exosomes-from-brain-tissue
#14
Laura J Vella, Benjamin J Scicluna, Lesley Cheng, Emma G Bawden, Colin L Masters, Ching-Seng Ang, Nicholas Willamson, Catriona McLean, Kevin J Barnham, Andrew F Hill
Extracellular vesicles, including exosomes, are released by all cells, including those of the nervous system. Capable of delivering lipid, protein and nucleic acids to both nearby and distal cells, exosomes have been hypothesized to play a role in progression of many diseases of the nervous system. To date, most analyses on the role of these vesicles in the healthy and diseased state have relied on studying vesicles from in vitro sources, such as conditioned cell culture media, or body fluids. Here we have taken a critical approach to the enrichment and characterization of exosomes from human frontal cortex...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28803104/exploration-of-a-mechanism-for-the-production-of-highly-unsaturated-fatty-acids-in-scenedesmus-sp-at-low-temperature-grown-on-oil-crop-residue-based-medium
#15
Qian Lu, Jun Li, Jinghan Wang, Kun Li, Jingjing Li, Pei Han, Paul Chen, Wenguang Zhou
The ability of algae to produce lipids comprising of unsaturated fatty acids varies with strains and culture conditions. This study investigates the effect of temperature on the production of unsaturated fatty acids in Scenedesmus sp. grown on oil crop residue based medium. At low temperature (10°C), synthesis of lipids compromising of high contents of unsaturated fatty acids took place primarily in the early stage while protein accumulation mainly occurred in the late stage. This stepwise lipid-protein synthesis process was found to be associated with the contents of acetyl-CoA and α-KG in the algal cells...
November 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28802999/primordial-membranes-more-than-simple-container-boundaries
#16
REVIEW
Martin M Hanczyc, Pierre-Alain Monnard
Cellular membranes, which are self-assembled bilayer structures mainly composed of lipids, proteins and conjugated polysaccharides, are the defining feature of cell physiology. It is likely that the complexity of contemporary cells was preceded by simpler chemical systems or protocells during the various evolutionary stages that led from inanimate to living matter. It is also likely that primitive membranes played a similar role in protocell 'physiology'. The composition of such ancestral membranes has been proposed as mixtures of single hydrocarbon chain amphiphiles, which are simpler versions of modern lipids...
August 10, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28802007/characterization-of-intrinsic-material-properties-of-a-model-lipoproteic-emulsion-gel-by-oscillatory-and-creep-compliance-rheometry
#17
Kyle S Okada, Wan-Yuan Kuo, Youngsoo Lee
The effects of varying formulation and processing parameters on rheological properties in a model lipid/protein-based emulsion gel were studied. Heat-set model lipoproteic emulsion gels were prepared with varying levels of protein, lipid, and NaCl contents and high pressure homogenization treatments. Small deformation oscillatory rheometry, creep compliance, and pore size analysis experiments were used to characterize intrinsic structural properties, matrix interactions, and microstructure. Creep compliance behavior of the gel system was successfully modeled by a four-component Burgers model...
August 12, 2017: Journal of Texture Studies
https://www.readbyqxmd.com/read/28782177/lipid-specificity-of-the-membrane-binding-domain-of-coagulation-factor-x
#18
Melanie P Muller, Yan Wang, James H Morrissey, Emad Tajkhorshid
BACKGROUND: Factor X (FX) binds to cell membranes in a highly phospholipid-dependent manner and, in complex with tissue factor and factor VIIa (FVIIa), initiates the clotting cascade. Experimental information concerning the membrane-bound structure of FX with atomic resolution has remained elusive due to the fluid nature of cellular membranes. FX is known to bind preferentially to phosphatidylserine (PS). OBJECTIVES: To develop the first membrane-bound model of FX-GLA domain to PS at atomic level, and to identify PS-specific binding sites of FX-GLA domain...
August 7, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28779844/saposin-lipoprotein-scaffolds-for-structure-determination-of-membrane-transporters
#19
Joseph A Lyons, Andreas Bøggild, Poul Nissen, Jens Frauenfeld
Membrane proteins depend on their natural lipid environment for function, which makes them more difficult to study in isolation. A number of approaches that mimic the lipid bilayer of biological membranes have been described (nanodiscs, SMALPs), enabling novel ways to assay activity and elucidate structures of this important class of proteins. More recently, the use of saposin A, a protein that is involved in lipid transport, to form Salipro (saposin-lipid-protein) complexes was demonstrated for a range of membrane protein targets (Frauenfeld et al...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28774891/sterol-transporters-at-membrane-contact-sites-regulate-torc1-and-torc2-signaling
#20
Andrew Murley, Justin Yamada, Bradley J Niles, Alexandre Toulmay, William A Prinz, Ted Powers, Jodi Nunnari
Membrane contact sites (MCSs) function to facilitate the formation of membrane domains composed of specialized lipids, proteins, and nucleic acids. In cells, membrane domains regulate membrane dynamics and biochemical and signaling pathways. We and others identified a highly conserved family of sterol transport proteins (Ltc/Lam) localized at diverse MCSs. In this study, we describe data indicating that the yeast family members Ltc1 and Ltc3/4 function at the vacuole and plasma membrane, respectively, to create membrane domains that partition upstream regulators of the TORC1 and TORC2 signaling pathways to coordinate cellular stress responses with sterol homeostasis...
September 4, 2017: Journal of Cell Biology
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