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https://www.readbyqxmd.com/read/29352609/induction-of-mitophagy-in-the-hei-oc1-auditory-cell-line-and-activation-of-the-atg12-lc3-pathway-in-the-organ-of-corti
#1
Cristian Setz, Anne-Sophie Benischke, Anna Catharina Pinho Ferreira Bento, Yves Brand, Soledad Levano, Franziska Paech, Katharina Leitmeyer, Daniel Bodmer
Autophagy is a highly evolutionary conserved quality control defense mechanism within cells, which has also been implicated in cell death processes. In the mammalian inner ear, autophagy has been shown to play a role during early morphogenesis as well as in adult cochlear hair cells exposed to ototoxic insults. Mitophagy, a selective autophagic cell process targeting mitochondria, hasn't been studied in the inner ear so far. On this work, we searched for molecular indicators of mitophagy within House Ear Institute-Organ of Corti-1 (HEI-OC1) cells as well as in the organ of Corti (OC)...
January 11, 2018: Hearing Research
https://www.readbyqxmd.com/read/29352320/high-level-production-and-purification-in-a-functional-state-of-an-extrasynaptic-gamma-aminobutyric-acid-type-a-receptor-containing-%C3%AE-4%C3%AE-3%C3%AE-subunits
#2
Xiaojuan Zhou, Rooma Desai, Yinghui Zhang, Wojciech J Stec, Keith W Miller, Youssef Jounaidi
The inhibitory γ-aminobutyric acid type A receptors are implicated in numerous physiological processes, including cognition and inhibition of neurotransmission, rendering them important molecular targets for many classes of drugs. Functionally, the entire GABAAR family of receptors can be subdivided into phasic, fast acting synaptic receptors, composed of α-, β- and γ-subunits, and tonic extrasynaptic receptors, many of which contain the δ-subunit in addition to α- and β-subunits. Whereas the subunit arrangement of the former group is agreed upon, that of the αβδ GABAARs remains unresolved by electrophysiological and pharmacological research...
2018: PloS One
https://www.readbyqxmd.com/read/29352170/plasma-proteomic-study-of-acute-mountain-sickness-susceptible-and-resistant-individuals
#3
Hui Lu, Rong Wang, Wenbin Li, Hua Xie, Chang Wang, Ying Hao, Yuhuan Sun, Zhengping Jia
Although extensive studies have focused on the development of acute mountain sickness (AMS), the exact mechanisms of AMS are still obscure. In this study, we used isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis to identify novel AMS-associated biomarkers in human plasma. After 9 hours of hypobaric hypoxia the abundance of proteins related to tricarboxylic acid (TCA) cycle, glycolysis, ribosome, and proteasome were significantly reduced in AMS resistant (AMS-) group, but not in AMS susceptible (AMS+) group...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352088/an-archaeal-fluoride-responsive-riboswitch-provides-an-inducible-expression-system-for-hyperthermophiles
#4
Michael Clayton Speed, Brett W Burkhart, Jonathan W Picking, Thomas J Santangelo
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated overexpression of native genes, allowed for the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and permitted the introduction of sequences encoding new proteins in these fast growing fermentative heterotrophs. Tightly controlled and easily manipulated systems permitting regulated gene expression are however limited for these hosts. Here we describe an alternative method for regulatory control reliant on a cis-encoded functional riboswitch in the model archaeon Thermococcus kodakarensis Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria, and similarly functions to regulate a component conserved fluoride export pathway...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29351928/mapping-and-quantification-of-over-2-000-o-linked-glycopeptides-in-activated-human-t-cells-with-isotope-targeted-glycoproteomics-isotag
#5
Christina M Woo, Peder J Lund, Andrew C Huang, Mark M Davis, Carolyn R Bertozzi, Sharon Pitteri
Post-translational modifications (PTMs) on proteins often function to regulate signaling cascades, with the activation of T cells during an adaptive immune response being a classic example.  Mounting evidence indicates that the modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc), the only mammalian glycan found on nuclear and cytoplasmic proteins, helps regulate T cell activation.  Yet, a mechanistic understanding of how O-GlcNAc functions in T cell activation remains elusive, partly because of the difficulties in mapping and quantifying O-GlcNAc sites...
January 19, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29351798/comparative-salivary-proteomics-analysis-of-children-with-and-without-dental-caries-using-the-itraq-mrm-approach
#6
Kun Wang, Yufei Wang, Xiuqing Wang, Qian Ren, Sili Han, Longjiang Ding, Zhongcheng Li, Xuedong Zhou, Wei Li, Linglin Zhang
BACKGROUND: Dental caries is a major worldwide oral disease afflicting a large proportion of children. As an important host factor of caries susceptibility, saliva plays a significant role in the occurrence and development of caries. The aim of the present study was to characterize the healthy and cariogenic salivary proteome and determine the changes in salivary protein expression of children with varying degrees of active caries, also to establish salivary proteome profiles with a potential therapeutic use against dental caries...
January 19, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29351065/measurement-of-binding-strength-between-prey-proteins-interacting-with-toxoplasma-gondii-sag1-and-sag2-using-isothermal-titration-calorimetry-itc
#7
Meng-Yee Lai, Yee-Ling Lau
Following the outcome from a previously performed yeast two-hybrid experiment, the binding strength between T. gondii SAG1 and SAG2 and their respective prey proteins were further confirmed in this study. The sag1, sag2 and their prey genes were amplified and cloned into a pGEMT vector. To express the recombinant proteins, the fragments were then subcloned into a pRSETA vector and transformed into E. coli BL21 (DE3) cells. The recombinant proteins were expressed optimally at 37°C and 1mM of IPTG. The 6X His-tag fusion proteins were purified, dialyzed and concentrated...
March 26, 2018: Acta Parasitologica
https://www.readbyqxmd.com/read/29350308/the-ppar%C3%AE-agonist-efatutazone-delays-invasive-progression-and-induces-differentiation-of-ductal-carcinoma-in-situ
#8
Virginie Ory, William B Kietzman, Jacob Boeckelman, Bhaskar V Kallakury, Anton Wellstein, Priscilla A Furth, Anna T Riegel
PURPOSE: Ductal carcinoma in situ (DCIS) is a pre-invasive lesion of the breast considered a precursor of invasive ductal carcinoma. This study aimed to determine whether activated PPARγ acts as a tumor suppressor in human DCIS progression. METHODS: We utilized the high-affinity PPARγ agonist, efatutazone, to activate endogenous PPARγ in a well-defined model for the progression of basal (triple negative) DCIS, MCFDCIS cells, cultured under 2D and 3D conditions...
January 19, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29350268/the-epitope-mediated-mmp-activation-assay-detection-and-quantification-of-the-activation-of-mmp2-in-vivo-in-the-zebrafish-embryo
#9
Emma J Jeffrey, Bryan D Crawford
Matrix remodeling is a consequence of tightly regulated matrix metalloproteinase (MMP) activity. MMPs are synthesized as inactive precursors with auto-inhibitory N-terminal propeptides, the proteolytic removal of which exposes the catalytic zinc ion, rendering the protease active. The regulation of MMP activation has been investigated primarily in tissue culture and biochemical assays that lack important biological context. Here we present the epitope-mediated MMP activation (EMMA) assay and use it to observe the activation of Mmp2 (gelatinase A) by endogenous mechanisms in the intact zebrafish embryo...
January 19, 2018: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/29350038/efficient-mass-spectral-analysis-of-active-transporters-overexpressed-in-escherichia-coli
#10
Mamiyo Kawakami, Narinobu Juge, Yuri Kato, Hiroshi Omote, Yoshinori Moriyama, Takaaki Miyaji
Structural analysis of purified active membrane proteins can be performed by mass spectrometry (MS). However, no large-scale expression systems for active eukaryotic membrane proteins are available. Moreover, because membrane proteins cannot easily be digested by trypsin and ionized, they are difficult to analyze by MS. Here, we developed a method for mass spectral analysis of eukaryotic membrane proteins combined to an overexpression system in Escherichia coli. Vesicular glutamate transporter 2 (VGLUT2/SLC17A6) with a soluble α-helical protein and histidine tag on the N- and C-terminus, respectively, was overexpressed in E...
January 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29349619/1h-15n-and-13c-chemical-shift-assignments-of-the-micelle-immersed-fat-c-terminal-fatc-domains-of-the-human-protein-kinases-ataxia-telangiectasia-mutated-atm-and-dna-dependent-protein-kinase-catalytic-subunit-dna-pkcs-fused-to-the-b1-domain-of-streptococcal
#11
Munirah S Abd Rahim, Lisa A M Sommer, Anja Wacker, Martin Schaad, Sonja A Dames
FAT C-terminal (FATC) is a circa 33 residue-long domain. It controls the kinase functionality in phosphatidylinositol-3 kinase-related kinases (PIKKs). Recent NMR- and CD-monitored interaction studies indicated that the FATC domains of all PIKKs can interact with membrane mimetics albeit with different preferences for membrane properties such as surface charge and curvature. Thus they may generally act as membrane anchoring unit. Here, we present the 1H, 15N, and 13C chemical shift assignments of the DPC micelle immersed FATC domains of the human PIKKs ataxia-telangiectasia mutated (ATM, residues 3024-3056) and DNA protein kinase catalytic subunit (DNA-PKcs, residues 4096-4128), both fused to the 56 residue long B1 domain of Streptococcal protein G (GB1)...
January 18, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29348539/characterization-of-a-novel-tectivirus-phage-toil-and-its-potential-as-an-agent-for-biolipid-extraction
#12
Jason J Gill, Baixin Wang, Emily Sestak, Ryland Young, Kung-Hui Chu
The oleaginous bacterium Rhodococcus opacus PD630 is metabolically diverse and can be cultivated on various renewable resources to serve as a sustainable triacylglycerol (TAG) feedstock for biodiesel production. Current methods for TAG extraction are costly, but infection of cultures by lytic bacteriophages (phages) may be a viable approach for achieving release of intracellular lipid from oleaginous bacteria such as R. opacus. This study reports the novel tectiviral phage Toil capable of releasing intracellular contents including a fluorescent protein marker and TAGs into the supernatant after phage infection of R...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348483/cell-type-specific-survey-of-epigenetic-modifications-by-tandem-chromatin-immunoprecipitation-sequencing
#13
Mari Mito, Mitsutaka Kadota, Kaori Tanaka, Yasuhide Furuta, Kuniya Abe, Shintaro Iwasaki, Shinichi Nakagawa
The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348432/genome-wide-association-study-of-self-reported-food-reactions-in-japanese-identifies-shrimp-and-peach-specific-loci-in-the-hla-dr-dq-gene-region
#14
Seik-Soon Khor, Ryoko Morino, Kazuyuki Nakazono, Shigeo Kamitsuji, Masanori Akita, Maiko Kawajiri, Tatsuya Yamasaki, Azusa Kami, Yuria Hoshi, Asami Tada, Kenichi Ishikawa, Maaya Hine, Miki Kobayashi, Nami Kurume, Naoyuki Kamatani, Katsushi Tokunaga, Todd A Johnson
Food allergy is an increasingly important health problem in the world. Several genome-wide association studies (GWAS) focused on European ancestry samples have identified food allergy-specific loci in the HLA class II region. We conducted GWAS of self-reported reactivity with common foods using the data from 11011 Japanese women and identified shrimp and peach allergy-specific loci in the HLA-DR/DQ gene region tagged by rs74995702 (P = 6.30 × 10-17, OR = 1.91) and rs28359884 (P = 2.3 × 10-12, OR = 1...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348144/a-crispr-tagging-based-screen-reveals-localized-players-in-wnt-directed-asymmetric-cell-division
#15
Jennifer K Heppert, Ariel M Pani, Allyson M Roberts, Daniel J Dickinson, Bob Goldstein
Oriented cell divisions are critical to establish and maintain cell fates and tissue organization. Diverse extracellular and intracellular cues have been shown to provide spatial information for mitotic spindle positioning, however, the molecular mechanisms by which extracellular signals communicate with cells to direct mitotic spindle positioning are largely unknown. In animal cells, oriented cell divisions are often achieved by the localization of force-generating, motor protein complexes to discrete cortical domains...
January 18, 2018: Genetics
https://www.readbyqxmd.com/read/29347906/expression-and-functional-analysis-of-the-propamocarb-related-gene-csdir16-in-cucumbers
#16
Chunhong Liu, Zhiwei Qin, Xiuyan Zhou, Ming Xin, Chunhua Wang, Dong Liu, Shengnan Li
BACKGROUND: Cucumber downy mildew is among the most important diseases that can disrupt cucumber production. Propamocarb, also known as propyl-[3-(dimethylamino)propyl]carbamate (PM), is a systemic carbamate fungicide pesticide that is widely applied in agricultural production because of its high efficiency of pathogens control, especially cucumber downy mildew. However, residual PM can remain in cucumbers after the disease has been controlled. To explore the molecular mechanisms of PM retention, cucumber cultivars 'D9320' (with the highest residual PM content) and 'D0351' (lowest residual PM content) were studied...
January 18, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29346752/epitranscriptomic-m6a-regulation-of-axon-regeneration-in-the-adult-mammalian-nervous-system
#17
Yi-Lan Weng, Xu Wang, Ran An, Jessica Cassin, Caroline Vissers, Yuanyuan Liu, Yajing Liu, Tianlei Xu, Xinyuan Wang, Samuel Zheng Hao Wong, Jessica Joseph, Louis C Dore, Qiang Dong, Wei Zheng, Peng Jin, Hao Wu, Bin Shen, Xiaoxi Zhuang, Chuan He, Kai Liu, Hongjun Song, Guo-Li Ming
N6-methyladenosine (m6A) affects multiple aspects of mRNA metabolism and regulates developmental transitions by promoting mRNA decay. Little is known about the role of m6A in the adult mammalian nervous system. Here we report that sciatic nerve lesion elevates levels of m6A-tagged transcripts encoding many regeneration-associated genes and protein translation machinery components in the adult mouse dorsal root ganglion (DRG). Single-base resolution m6A-CLIP mapping further reveals a dynamic m6A landscape in the adult DRG upon injury...
January 17, 2018: Neuron
https://www.readbyqxmd.com/read/29346583/datamed-an-open-source-discovery-index-for-finding-biomedical-datasets
#18
Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu
Objective: Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain. Materials and Methods: DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium...
January 13, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29346282/smartphone-based-cooperative-indoor-localization-with-rfid-technology
#19
Fernando Seco, Antonio R Jiménez
In GPS-denied indoor environments, localization and tracking of people can be achieved with a mobile device such as a smartphone by processing the received signal strength (RSS) of RF signals emitted from known location beacons (anchor nodes), combined with Pedestrian Dead Reckoning (PDR) estimates of the user motion. An enhacement of this localization technique is feasible if the users themselves carry additional RF emitters (mobile nodes), and the cooperative position estimates of a group of persons incorporate the RSS measurements exchanged between users...
January 18, 2018: Sensors
https://www.readbyqxmd.com/read/29345800/haplotype-based-genotyping-by-sequencing-in-oat-genome-research
#20
Wubishet A Bekele, Charlene P Wight, Shiaoman Chao, Catherine J Howarth, Nicholas A Tinker
In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel...
January 18, 2018: Plant Biotechnology Journal
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