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https://www.readbyqxmd.com/read/28934756/tumor-necrosis-factor-receptor-mediates-fibroblast-growth-factor-inducible-14-signaling
#1
Xuening Wang, Shengxiang Xiao, Yumin Xia
Tumor necrosis factor (TNF)-related weak inducer of apoptosis (TWEAK) engages its sole receptor, fibroblast growth factor-inducible 14 (Fn14), which participates in various inflammatory and immunologic processes. TWEAK/Fn14 interaction induces different cell fates depending on the local microenvironment, which correlates with certain expression profiles of TNF receptors (TNFR). The predominant expression of TNFR1 or TNFR2 facilitates cell death or proliferation, respectively, on TWEAK/Fn14 activation. TNFR-associated factors (TRAF) interact with Fn14, cellular inhibitor of apoptosis protein (cIAP)-1, and TNFR, consequently transducing signals from TWEAK to downstream cytokines and cell cycle mediators...
September 21, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28934693/enzyme-classification-using-multiclass-support-vector-machine-and-feature-subset-selection
#2
Debasmita Pradhan, Sudarsan Padhy, Biswajit Sahoo
Proteins are the macromolecules responsible for almost all biological processes in a cell. With the availability of large number of protein sequences from different sequencing projects, the challenge with the scientist is to characterize their functions. As the wet lab methods are time consuming and expensive, many computational methods such as FASTA, PSI-BLAST, DNA microarray clustering, and Nearest Neighborhood classification on protein-protein interaction network have been proposed. Support vector machine is one such method that has been used successfully for several problems such as protein fold recognition, protein structure prediction etc...
August 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28934692/identification-of-key-genes-and-pathways-and-therapeutic-agents-in-cadmium-treated-liver-cells-a-bioinformatics-study
#3
Liang Zhang, Yi Huang, Zhen Yu, Mengmeng Shao, Yunbo Luo, Yi Zhu
Evidence indicates that Cadmium (Cd) can accumulate in liver, which results in acute or chronic cell damage with unclear complex mechanisms. Thus, we aimed to explore the possible molecules and pathways by using bioinformatics methods Consequently, two datasets (GSE8865 and GSE31286) were retrieved and the differentially expressed genes (DEGs) were screened out. The intersection of the DEGs included seven up-regulated and forty-three down-regulated genes, which were mainly enriched in biological cell proliferation items, and were enriched in several metabolism-related pathways...
September 14, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28934646/clerodane-diterpenoids-from-scutellaria-formosana-with-inhibitory-effects-on-no-production-and-interactions-with-inos-protein
#4
Peixia Wang, Feng Liu, Xueyuan Yang, Yue Liang, Shen Li, Guochen Su, Da-Qing Jin, Yasushi Ohizumi, Jing Xu, Yuanqiang Guo
A phytochemical study on Scutellaria formosana afforded five previously undescribed spiro-diterpenoids, scutellapenes A-E. The structures were elucidated on the basis of extensive 1D and 2D NMR spectroscopic data analysis, and the absolute configurations of these compounds were established by the time-dependent density functional theory (TDDFT) electronic circular dichroism (ECD) calculations. Scutellapenes B-E possess a spiro-diterpenoid skeleton. All of the compounds showed inhibitory effects on LPS-induced nitric oxide (NO) production in murine microglial BV-2 cells...
September 18, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28934506/clip-seq-analysis-of-multi-mapped-reads-discovers-novel-functional-rna-regulatory-sites-in-the-human-transcriptome
#5
Zijun Zhang, Yi Xing
Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934503/a-novel-requirement-for-drosha-in-maintenance-of-mammalian-cg-methylation
#6
Athanasia Stathopoulou, Jyoti B Chhetri, John C Ambrose, Pierre-Olivier Estève, Lexiang Ji, Hediye Erdjument-Bromage, Guoqiang Zhang, Thomas A Neubert, Sriharsa Pradhan, Javier Herrero, Robert J Schmitz, Steen K T Ooi
In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocessor component DROSHA as a novel DNMT1-interactor. Drosha-deficient embryonic stem (ES) cells display genomic hypomethylation that is not accounted for by changes in the levels of DNMT proteins...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934502/blocking-the-reca-activity-and-sos-response-in-bacteria-with-a-short-%C3%AE-helical-peptide
#7
Alexander Yakimov, Georgii Pobegalov, Irina Bakhlanova, Mikhail Khodorkovskii, Michael Petukhov, Dmitry Baitin
The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934500/a-synthetic-dna-binding-inhibitor-of-sox2-guides-human-induced-pluripotent-stem-cells-to-differentiate-into-mesoderm
#8
Junichi Taniguchi, Ganesh N Pandian, Takuya Hidaka, Kaori Hashiya, Toshikazu Bando, Kyeong Kyu Kim, Hiroshi Sugiyama
Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioactive synthetic DNA-binding inhibitors, targeting key cell fate-controlling genes such as SOX2, are yet available. Here, we demonstrate a novel DNA-based chemical approach to guide the differentiation of hiPSCs using pyrrole-imidazole polyamides (PIPs), which are sequence-selective DNA-binding synthetic molecules...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934484/regulation-of-hur-structure-and-function-by-dihydrotanshinone-i
#9
Preet Lal, Linda Cerofolini, Vito Giuseppe D'Agostino, Chiara Zucal, Carmelo Fuccio, Isabelle Bonomo, Erik Dassi, Stefano Giuntini, Danilo Di Maio, Vikalp Vishwakarma, Ranjan Preet, Sha Neisha Williams, Max S Fairlamb, Rachel Munk, Elin Lehrmann, Kotb Abdelmohsen, Saioa R Elezgarai, Claudio Luchinat, Ettore Novellino, Alessandro Quattrone, Emiliano Biasini, Leonardo Manzoni, Myriam Gorospe, Dan A Dixon, Pierfausto Seneci, Luciana Marinelli, Marco Fragai, Alessandro Provenzani
The Human antigen R protein (HuR) is an RNA-binding protein that recognizes U/AU-rich elements in diverse RNAs through two RNA-recognition motifs, RRM1 and RRM2, and post-transcriptionally regulates the fate of target RNAs. The natural product dihydrotanshinone-I (DHTS) prevents the association of HuR and target RNAs in vitro and in cultured cells by interfering with the binding of HuR to RNA. Here, we report the structural determinants of the interaction between DHTS and HuR and the impact of DHTS on HuR binding to target mRNAs transcriptome-wide...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934483/the-fused-snoal_2-domain-in-the-mycobacterium-tuberculosis-sigma-factor-%C3%AF-j-modulates-promoter-recognition
#10
Kapil Goutam, Arvind K Gupta, Balasubramanian Gopal
Extra-cytoplasmic function (ECF) σ-factors are widespread in bacteria, linking environmental stimuli with changes in gene expression. These transcription factors span several phylogenetically distinct groups and are remarkably diverse in their activation and regulatory mechanisms. Here, we describe the structural and biochemical features of a Mycobacterium tuberculosis ECF factor σJ that suggests that the SnoaL_2 domain at the C-terminus can modulate the activity of this initiation factor in the absence of a cognate regulatory anti-σ factor...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934470/monitoring-replication-protein-a-rpa-dynamics-in-homologous-recombination-through-site-specific-incorporation-of-non-canonical-amino-acids
#11
Nilisha Pokhrel, Sofia Origanti, Eric Parker Davenport, Disha Gandhi, Kyle Kaniecki, Ryan A Mehl, Eric C Greene, Chris Dockendorff, Edwin Antony
An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934384/short-syndrome-due-to-a-novel-de-novo-mutation-in-prkce-protein-kinase-c%C3%A9-impairing-torc2-dependent-akt-activation
#12
Diana Alcantara, Frances Elmslie, Martine Tetreault, Eric Bareke, Taila Hartley, Jacek Majewski, Kym Boycott, A Micheil Innes, David A Dyment, Mark O'Driscoll
SHORT syndrome is a rare, recognizable syndrome resulting from heterozygous mutations in PIK3R1 encoding a regulatory subunit of phosphoinositide-3-kinase (PI3K). The condition is characterized by short stature, intrauterine growth restriction, lipoatrophy and a facial gestalt involving a triangular face, deep set eyes, low hanging columella and small chin. PIK3R1 mutations in SHORT syndrome result in reduced signaling through the PI3K-AKT-mTOR pathway. We performed whole exome sequencing for an individual with clinical features of SHORT syndrome but negative for PIK3R1 mutation and her parents...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28934381/carboxysomes-metabolic-modules-for-co2-fixation
#13
Aiko Turmo, C Raul Gonzalez-Esquer, Cheryl A Kerfeld
The carboxysome is a bacterial microcompartment encapsulating the enzymes carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase. As the site of CO2 fixation, it serves an essential role in the carbon dioxide concentrating mechanism of many chemoautotrophs and all cyanobacteria. Carboxysomes and other bacterial microcompartments self-assemble through specific protein-protein interactions that are typically mediated by conserved protein domains. In this review, we frame our current understanding of carboxysomes in the context of their component protein domains with their inherent function as the 'building blocks' of carboxysomes...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28934355/study-of-myelin-structure-changes-during-the-nerve-fibers-demyelination
#14
Natalia N Rodionova, Elvin S Allakhverdiev, Georgy V Maksimov
Raman, NMR and EPR spectroscopy and electrophysiology methods were used to investigate the excitability and the packaging of myelin lipid layers and its viscosity during nerve exposure to pronase E. It was established that during exposure of nerve to pronase E the action potential (AP) conduction velocity and the Schwann cell (SC) (or myelin) water ordering increases, but the nerve myelin refractive index and internode incisions numbers decrease. This effect included two periods-short- and long-time period, probably, because the first one depends on SC protein changes and the second one-on the nerve fiber internode demyelination...
2017: PloS One
https://www.readbyqxmd.com/read/28934328/the-human-vgf-derived-bioactive-peptide-tlqp-21-binds-heat-shock-71-kda-protein-8-hspa8-on-the-surface-of-sh-sy5y-cells
#15
Shamim Akhter, Sandipan Chakraborty, Daniela Moutinho, Elia Álvarez-Coiradas, Isaac Rosa, Juan Viñuela, Eduardo Domínguez, Angel García, Jesús R Requena
VGF (non-acronymic)is a secreted chromogranin/secretogranin that gives rise to a number of bioactive peptides by a complex proteolysis mechanism. VGF-derived peptides exert an extensive array of biological effects in energy metabolism, mood regulation, pain, gastric secretion function, reproduction and, perhaps, cancer. It is therefore surprising that very little is known about receptors and binding partners of VGF-derived peptides and their downstream molecular mechanisms of action. Here, using affinity chromatography and mass spectrometry-based protein identification, we have identified the heat shock cognate 71 kDa protein A8 (HSPA8)as a binding partner of human TLQP-21 on the surface of human neuroblastomaSH-SY5Y cells...
2017: PloS One
https://www.readbyqxmd.com/read/28934301/microwave-bio-sensor-based-on-symmetrical-split-ring-resonator-with-spurline-filters-for-therapeutic-goods-detection
#16
Rammah A Alahnomi, Z Zakaria, E Ruslan, S R Ab Rashid, Amyrul Azuan Mohd Bahar, Azizah Shaaban
A novel symmetrical split ring resonator (SSRR) based microwave sensor with spurline filters for detecting and characterizing the properties of solid materials has been developed. Due to the weak perturbation in the interaction of material under test (MUT) and planar microwave sensor, spurline filters were embedded to the SSRR microwave sensor which effectively enhanced Q-factor with suppressing the undesired harmonic frequency. The spurline filter structures force the presented sensor to resonate at a fundamental frequency of 2...
2017: PloS One
https://www.readbyqxmd.com/read/28934288/purification-of-rabbit-serum-histidine-proline-rich-glycoprotein-via-preparative-gel-electrophoresis-and-characterization-of-its-glycosylation-patterns
#17
Anna Katharina Weyrauch, Mario Jakob, Angelika Schierhorn, Ralf Bernd Klösgen, Dariush Hinderberger
Histidine-Proline-rich Glycoprotein (HPRG) is a plasma protein of vertebrates and several marine bivalves. Due to its multidomain structure consisting of several regions HPRG can interact with a variety of ligands, however the exact physiological role has not been discovered yet. Past purification approaches out of plasma or serum often led to co-purification of other proteins so that for a profound understanding of the function it is important to obtain a protein of high purity. Recent purification strategies were based upon metale chelate affinity chromatography followed by anion exchange chromatography or size exclusion chromatography, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28934149/oncolytic-reovirus-infection-is-facilitated-by-the-autophagic-machinery
#18
Vera Kemp, Iris J C Dautzenberg, Ronald W Limpens, Diana J M van den Wollenberg, Rob C Hoeben
Mammalian reovirus is a double-stranded RNA virus that selectively infects and lyses transformed cells, making it an attractive oncolytic agent. Despite clinical evidence for anti-tumor activity, its efficacy as a stand-alone therapy remains to be improved. The success of future trials can be greatly influenced by the identification and the regulation of the cellular pathways that are important for reovirus replication and oncolysis. Here, we demonstrate that reovirus induces autophagy in several cell lines, evident from the formation of Atg5-Atg12 complexes, microtubule-associated protein 1 light chain 3 (LC3) lipidation, p62 degradation, the appearance of acidic vesicular organelles, and LC3 puncta...
September 21, 2017: Viruses
https://www.readbyqxmd.com/read/28934148/tomato-leaf-curl-new-delhi-virus-an-emerging-virus-complex-threatening-vegetable-and-fiber-crops
#19
REVIEW
Enrique Moriones, Shelly Praveen, Supriya Chakraborty
The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent. However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin. Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade...
September 21, 2017: Viruses
https://www.readbyqxmd.com/read/28934144/the-recognition-of-calmodulin-to-the-target-sequence-of-calcineurin-a-novel-binding-mode
#20
Chia-Lin Chyan, Deli Irene, Sin-Mao Lin
Calcineurin (CaN) is a Ca(2+)/calmodulin-dependent Ser/Thr protein phosphatase, which plays essential roles in many cellular and developmental processes. CaN comprises two subunits, a catalytic subunit (CaN-A, 60 kDa) and a regulatory subunit (CaN-B, 19 kDa). CaN-A tightly binds to CaN-B in the presence of minimal levels of Ca(2+), but the enzyme is inactive until activated by CaM. Upon binding to CaM, CaN then undergoes a conformational rearrangement, the auto inhibitory domain is displaced and thus allows for full activity...
September 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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