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https://www.readbyqxmd.com/read/28542806/structural-and-functional-study-of-a-simple-rapid-and-label-free-dnazyme-based-dna-biosensor-for-optimization-activity
#1
Narges Shahbazi, Saman Hosseinkhani, Khosro Khajeh, Bijan Ranjbar
Peroxidase-mimicking DNAzyme has a potential to self-assemble into a G-quadruplex and shows peroxidase activity. In comparison to proteins, peroxidase-mimicking DNAzyme is less expensive and more stable. Herein, it is used in fabricating non-labeling biosensors. This paper investigates the structural and functional properties of a DNA biosensor based on split DNAzyme with a detection limit in nM range (9.48 nM). Two halves of DNAzyme were linked by a complementary sequence of DNA target. Hybridization of the DNA target pulled two DNAzyme halves apart and peroxidase activity decreased...
May 20, 2017: Biopolymers
https://www.readbyqxmd.com/read/28540354/data-on-the-exon-intron-organization-of-genes-coding-for-b-cell-receptor-like-proteins
#2
Sergey Y Morozov, Anna V Pankratenko, Anastasia K Atabekova, Andrey G Solovyev
B-cell receptor-associated protein (BAP) family plays important roles in the ER homeostasis and stress responses of eukaryotic cells [1]. We reported the analysis of plant BAP-like (PBL) genes and the encoded proteins of higher land plants [2]. The origin and functional divergence of these genes among all eukaryotes, however, are poorly studied, which impedes our understanding of the functional relationships and diversity among BAP-like proteins. One possible reason for the potential functional diversity may be the differences in the exon-intron structure of PBL genes...
June 2017: Data in Brief
https://www.readbyqxmd.com/read/28534849/evaluation-and-comparison-of-the-pathogenicity-and-host-immune-responses-induced-by-a-g2b-taiwan-porcine-epidemic-diarrhea-virus-strain-pintung-52-and-its-highly-cell-culture-passaged-strain-in-conventional-5-week-old-pigs
#3
Yen-Chen Chang, Chi-Fei Kao, Chia-Yu Chang, Chian-Ren Jeng, Pei-Shiue Tsai, Victor Fei Pang, Hue-Ying Chiou, Ju-Yi Peng, Ivan-Chen Cheng, Hui-Wen Chang
A genogroup 2b (G2b) porcine epidemic diarrhea virus (PEDV) Taiwan Pintung 52 (PEDVPT) strain was isolated in 2014. The pathogenicity and host antibody responses elicited by low-passage (passage 5; PEDVPT-P5) and high-passage (passage 96; PEDVPT-P96) PEDVPT strains were compared in post-weaning PEDV-seronegative pigs by oral inoculation. PEDVPT-P5-inoculation induced typical diarrhea during 1-9 days post inoculation with fecal viral shedding persisting for 26 days. Compared to PEDVPT-P5, PEDVPT-P96 inoculation induced none-to-mild diarrhea and lower, delayed fecal viral shedding...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28528213/optimal-electrostatic-interactions-between-substrate-and-protein-are-essential-for-radical-chemistry-in-ornithine-4-5-aminomutase
#4
Caitlyn Makins, Douglas A Whitelaw, Michael McGregor, Alix Petit, Robert G Mothersole, Kathleen E Prosser, Kirsten R Wolthers
Ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii is an adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes a 1,2-amino shift, interconverting D-ornithine and 2S, 4R-diaminopentanoate. The reaction occurs via a radical-based mechanism whereby a PLP-bound substrate radical undergoes intramolecular isomerization via an azacyclopropylcarbinyl radical intermediate. Herein, we investigated the catalytic role of active site residues that form non-covalent interactions with PLP and/or substrate, D-ornithine...
May 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28527439/preferential-binding-effects-on-protein-structure-and-dynamics-revealed-by-coarse-grained-monte-carlo-simulation
#5
R B Pandey, D J Jacobs, B L Farmer
The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28526530/insights-into-the-early-stage-of-pinus-nigra-arn-somatic-embryogenesis-using-discovery-proteomics
#6
Katarína Klubicová, Lubica Uvácková, Maksym Danchenko, Peter Nemecek, Ludovít Skultéty, Ján Salaj, Terézia Salaj
The somatic embryogenesis in conifers represents a suitable model of plant regeneration system facilitating studies of fundamental aspects of an early development as well as in vitro micropropagation. The aim of our study was to deeper understand the somatic embryogenesis in the conifer tree Pinus nigra Arn. Comparative proteomic analysis based on 2D-PAGE in 1) proliferating embryogenic tissues (E) initiated from immature zygotic embryos, 2) non-embryogenic calli (NEC) initiated from cotyledons of somatic seedlings of the same genotypes, 3) embryogenic tissues that lost the maturation capacity (E-L) of two cell lines (E362, E366)...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28524918/urotensin-ii-peptidomimetic-incorporating-a-non-reducible-1-5-triazole-disulfide-bond-reveals-a-pseudo-irreversible-covalent-binding-mechanism-to-the-urotensin-g-protein-coupled-receptor
#7
Salvatore Pacifico, Aidan Kerckhoffs, Andrew J Fallow, Rachel E Foreman, Remo Guerrini, John McDonald, David G Lambert, Andrew G Jamieson
The urotensin-II receptor (UTR) is a class A GPCR that predominantly binds to the pleiotropic cyclic peptide urotensin-II (U-II). U-II is constrained by a disulfide bridge that induces a β-turn structure and binds pseudo-irreversibly to UTR and is believed to result in a structural rearrangement of the receptor. However, it is not well understood how U-II binds pseudo-irreversibly and the nature of the reorganization of the receptor that results in G-protein activation. Here we describe a series of U-II peptidomimetics incorporating a non-reducible disulfide bond structural surrogate to investigate the feasibility that native U-II binds to the G protein-coupled receptor through disulfide bond shuffling as a mechanism of covalent interaction...
May 19, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28524877/optimized-fragmentation-schemes-and-data-analysis-strategies-for-proteome-wide-cross-link-identification
#8
Fan Liu, Philip Lössl, Richard Scheltema, Rosa Viner, Albert J R Heck
We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ∼1% false discovery rate...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28510595/structural-adaptations-of-octaheme-nitrite-reductases-from-haloalkaliphilic-thioalkalivibrio-bacteria-to-alkaline-ph-and-high-salinity
#9
Anna Popinako, Mikhail Antonov, Alexey Tikhonov, Tamara Tikhonova, Vladimir Popov
Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl). To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed...
2017: PloS One
https://www.readbyqxmd.com/read/28507418/spatial-pattern-of-foot-and-mouth-disease-virus-serotypes-in-north-central-nigeria
#10
Yiltawe Simwal Wungak, Olayinka O Ishola, Babasola O Olugasa, David D Lazarus, David O Ehizibolo, Hussaini G Ularamu
AIM: This study aimed to determine the foot-and-mouth disease virus (FMDV) serotypes circulating, the prevalence of FMDV serotypes, and the spatial distribution of FMDV among sedentary and pastoral cattle herds in the North-Central Nigeria. MATERIALS AND METHODS: A cross-sectional study was undertaken, during which a total of 155 sera that tested positive for foot-and-mouth disease (FMD) 3ABC non-structural protein antibodies were selected and screened for FMD structural protein serotypes, A, O, SAT 1, and SAT 2 using a solid-phase competitive enzyme-linked immunosorbent assay (ELISA)...
April 2017: Veterinary World
https://www.readbyqxmd.com/read/28506210/sucrose-non-ferment-1-related-protein-kinase-2-snrk2-genes-could-mediate-the-stress-responses-in-potato-solanum-tuberosum-l
#11
Jiangping Bai, Juan Mao, Hongyu Yang, Awais Khan, Aqi Fan, Siyan Liu, Junlian Zhang, Di Wang, Huijuan Gao, Jinlin Zhang
BACKGROUND: The SnRKs (sucrose non-fermenting 1 related protein kinase) are a gene family coding for Ser/Thr protein kinases and play important roles in linking the tolerance and metabolic responses of plants to abiotic stresses. To date, no genome-wide characterization of the sucrose non-ferment 1 related protein kinase 2 (SnRK2) subfamily has been conducted in potato (Solanum tuberosum L.). RESULTS: In this study, eight StSnRK2 genes (StSnRK2.1- StSnRK2.8) were identified in the genome of the potato (Solanum tuberosum L...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28506209/peptides-mimicking-viral-proteins-of-porcine-circovirus-type-2-were-profiled-by-the-spectrum-of-mouse-anti-pcv2-antibodies
#12
Ling-Chu Hung, Cheng-Yao Yang, Ivan-Chen Cheng
BACKGROUND: Porcine circovirus 2 (PCV2) is a small, non-enveloped DNA virus causing swine lymphocyte depletion and severe impact on the swine industry. The aim of this study was to evaluate the antigenicity and immunogenicity of specific peptides, and seeking the potential candidate of PCV2 peptide-based vaccine. It's initiating from peptides reacting with PCV2-infected pig sera and peptide-immunized mouse sera. RESULTS: The data showed that the sera from PCV2-infected pigs could react with the N-terminal (C1), middle region (C2), and C-terminal peptide (C3) of PCV2 capsid protein (CP), ORF3 protein (N1), ORF6 protein (N2) and ORF9 protein (N3)...
May 15, 2017: BMC Immunology
https://www.readbyqxmd.com/read/28502793/salt-mediated-oligomerization-of-the-mouse-prion-protein-monitored-by-real-time-nmr
#13
Ishita Sengupta, Suhas H Bhate, Ranabir Das, Jayant B Udgaonkar
The prion protein forms ß-rich soluble oligomers in vitro at pH4 in the presence of physiological concentrations of salt. In the absence of salt, oligomerization and misfolding does not take place in an experimentally tractable timescale. While it is well established that a lowering of pH facilitates misfolding and oligomerization of this protein, the role of salt remains poorly understood. Here, solution-state NMR was used to probe perturbations in the monomeric mouse prion protein moPrP) structure immediately upon salt-addition, prior to the commencement of the oligomerization reaction...
May 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28501776/inhibition-of-senp3-by-urb597-ameliorates-neurovascular-unit-dysfunction-in-rats-with-chronic-cerebral-hypoperfusion
#14
Da-Peng Wang, Ke-Jia Liu, Graham Kasper, Qi Lin, Jian Hai
Disruption of the neurovascular unit (NVU), induced by chronic cerebral hypoperfusion (CCH), has been broadly found in various neurological disorders. SUMO-specific protease 3 (SENP3) is expressed in neurons, astrocytes, and microglia, and regulates a variety of cell events. However, whether SENP3 is involved in neurovascular injury under the condition of CCH is still elusive. To address this issue, we investigated the effect of the fatty acid amide hydrolase (FAAH) inhibitor URB597 on NVU and the role of SENP3 in this process, as well as the underling mechanisms...
May 11, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28499188/ptp1b-inhibitors-from-selaginella-tamariscina-beauv-spring-and-their-kinetic-properties-and-molecular-docking-simulation
#15
Duc Dat Le, Duc Hung Nguyen, Bing Tian Zhao, Su Hui Seong, Jae Sue Choi, Seok Kyu Kim, Jeong Ah Kim, Byung Sun Min, Mi Hee Woo
Diabetes is one of the most popular worldwide diseases, regulated by the defects in insulin secretion, insulin action, or both. The overexpression of protein tyrosine phosphatase 1B (PTP1B) was found to down-regulate the insulin-receptor activation. PTP1B has been known as a strategy for the treatment of diabetes via the regulation of insulin signal transduction pathway. Herein, we investigated the PTP1B inhibitors isolated from natural sources. The chemical investigation of Selaginella tamariscina (Beauv.) Spring revealed seven unsaturated alkynyl phenols 1-7, four new selaginellins T-W 1-4 together with three known compounds 5-7 isolated from the aerial parts...
May 2, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28499021/protein-only-rnase-p-function-in-escherichia-coli-viability-processing-defects-and-differences-between-prorp-isoenzymes
#16
Markus Gößringer, Marcus Lechner, Nadia Brillante, Christoph Weber, Walter Rossmanith, Roland K Hartmann
The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and the two nuclear (AtPRORP2,3) single-polypeptide RNase P isoenzymes from Arabidopsis thaliana confer viability to Escherichia coli cells with a lethal knockdown of its endogenous RNA-based RNase P. RNA-Seq revealed that AtPRORP1, compared with bacterial RNase P or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli...
May 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28496027/expression-profile-of-matricellular-proteins-in-hypertrophied-right-ventricle-of-monocrotaline-induced-pulmonary-hypertensive-rats
#17
Keisuke Imoto, Muneyoshi Okada, Hideyuki Yamawaki
Matricellular proteins, a non-structural extracellular matrix (ECM) component, bind to and modulate various molecules including growth factor, cytokine, protease, other ECM components and cell membrane receptors. While most matricellular proteins are hardly expressed in normal adult tissue, they are re-expressed in heart tissue during cardiac diseases. The present study aimed to clarify the mRNA expression profile of matricellular proteins [secreted protein acidic and rich in cysteine: SPARC, hevin, thrombospondin (TSP)-1, -2 and -4, CCN1 and 5, tenascin (Tn)C and N, periostin and osteopontin (OPN)] in hypertrophied right ventricle (RV) of monocrotaline (MCT)-induced pulmonary hypertensive rats...
May 11, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28492611/the-effect-of-topical-treatments-for-crs-on-the-sinonasal-epithelial-barrier
#18
M Ramezanpour, A Rayan, J L P Smith, S Vreugde
BACKGROUND: Several topical treatments are used in the management of Chronic Rhinosinusitis (CRS), some of which the safety and efficacy has yet to be determined. The purpose of this study was to investigate the effect of commonly used topical treatments on the sinonasal epithelial barrier. METHODS: Normal saline (0.9% Sodium Chloride), hypertonic saline (3% Sodium Chloride), FESS Sinu-Cleanse Hypertonic, FLO Sinus Care and Budesonide 1 mg/ 2 ml were applied to the apical side of air-liquid interface (ALI) cultures of primary human nasal epithelial cells (HNECs) from CRS patients (n=3) and non-CRS controls (n=3) for 24 hours...
May 10, 2017: Rhinology
https://www.readbyqxmd.com/read/28482466/synthesis-structure-elucidation-and-biological-evaluation-of-triple-bridged-dinuclear-copper-ii-complexes-as-anticancer-and-antioxidant-anti-inflammatory-agents
#19
Z Boulsourani, S Katsamakas, G D Geromichalos, V Psycharis, C P Raptopoulou, D Hadjipavlou-Litina, E Yiannaki, C Dendrinou-Samara
Seeking for copper based metallo-therapeutics, three triple bridged dinuclear copper(II) complexes [Cu2(μ2-L2)(bipy)2(μ2-OH)(μ2-H2O)](NO3)2·H2O (1·H2O), [Cu2(μ2-L2)(bipy)2(μ2-OH)(μ2-NO3)](NO3)·0.6MeOH·0.4H2O (2·0.6MeOH·0.4H2O) and [Cu2(μ2-L1)(bipy)2(μ2-OH)(μ2-NO3)(H2O)](NO3)·2H2O (3·2H2O) where L2=2-thiophene acetato, L1=2-thiophene carboxylato and bipy=2,2'-bipyridine were synthesized and structurally characterized. The complexes were subjected in vitro to a pharmacochemical evaluation for their antioxidant/anti-inflammatory activity, cytotoxicity and efficacy against human ovarian, lung, colon, breast, kidney and cervical cancer cell lines along with non tumor human lung and breast cell lines...
July 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28476069/elac-3-12-di-o-acetyl-8-o-tigloilingol-a-plant-derived-lathyrane-diterpene-induces-subventricular-zone-neural-progenitor-cell-proliferation-through-protein-kinase-c-beta-activation
#20
Maribel Murillo-Carretero, Noelia Geribaldi-Doldán, Eugenia Flores-Giubi, Francisco García-Bernal, Elkin A Navarro, Manuel Carrasco-Viñuela, Antonio J Macías-Sánchez, Pilar Herrero-Foncubierta, Antonio Delgado-Ariza, Cristina Verástegui, Jesús Domínguez-Riscart, Mourad Daoubi, Rosario Hernández-Galán, Carmen Castro
BACKGROUND AND PURPOSE: Pharmacological strategies aimed to facilitate neuronal renewal in the adult brain, by promoting endogenous neurogenesis, constitute promising therapeutic options for pathologic or traumatic brain lesions. We have previously shown that non-tumor-promoting PKC-activating compounds (12-deoxyphorbols) promote adult neural progenitor cell (NPC) proliferation in vitro and in vivo, enhancing the endogenous neurogenic response of the brain to a traumatic injury. Here, we show for the first time that a diterpene with lathyrane skeleton can also activate PKC and promote NPC proliferation...
May 5, 2017: British Journal of Pharmacology
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