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https://www.readbyqxmd.com/read/29051762/specific-pathogen-recognition-by-multiple-innate-immune-sensors-in-an-invertebrate
#1
Guillaume Tetreau, Silvain Pinaud, Anaïs Portet, Richard Galinier, Benjamin Gourbal, David Duval
Detection of pathogens by all living organisms is the primary step needed to implement a coherent and efficient immune response. This implies a mediation by different soluble and/or membrane-anchored proteins related to innate immune receptors called PRRs (pattern-recognition receptors) to trigger immune signaling pathways. In most invertebrates, their roles have been inferred by analogy to those already characterized in vertebrate homologs. Despite the induction of their gene expression upon challenge and the presence of structural domains associated with the detection of pathogen-associated molecular patterns in their sequence, their exact role in the induction of immune response and their binding capacity still remain to be demonstrated...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29050215/proteomics-analysis-of-bladder-cancer-invasion-targeting-eif3d-for-therapeutic-intervention
#2
Agnieszka Latosinska, Marika Mokou, Manousos Makridakis, William Mullen, Jerome Zoidakis, Vasiliki Lygirou, Maria Frantzi, Ioannis Katafigiotis, Konstantinos Stravodimos, Marie C Hupe, Maciej Dobrzynski, Walter Kolch, Axel S Merseburger, Harald Mischak, Maria G Roubelakis, Antonia Vlahou
Patients with advanced bladder cancer have poor outcomes, indicating a need for more efficient therapeutic approaches. This study characterizes proteomic changes underlying bladder cancer invasion aiming for the better understanding of disease pathophysiology and identification of drug targets. High resolution liquid chromatography coupled to tandem mass spectrometry analysis of tissue specimens from patients with non-muscle invasive (NMIBC, stage pTa) and muscle invasive bladder cancer (MIBC, stages pT2+) was conducted...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29046682/cyclic-nucleotide-monophosphates-and-their-cyclases-in-plant-signaling
#3
REVIEW
Chris Gehring, Ilona S Turek
The cyclic nucleotide monophosphates (cNMPs), and notably 3',5'-cyclic guanosine monophosphate (cGMP) and 3',5'-cyclic adenosine monophosphate (cAMP) are now accepted as key signaling molecules in many processes in plants including growth and differentiation, photosynthesis, and biotic and abiotic defense. At the single molecule level, we are now beginning to understand how cNMPs modify specific target molecules such as cyclic nucleotide-gated channels, while at the systems level, a recent study of the Arabidopsis cNMP interactome has identified novel target molecules with specific cNMP-binding domains...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29046456/viperin-targets-flavivirus-virulence-by-inducing-assembly-of-non-infectious-capsid-particles
#4
Kirstin Vonderstein, Emma Nilsson, Philipp Hubel, Lars Nygård Skalman, Arunkumar Upadhyay, Jenny Pasto, Andreas Pichlmair, Richard Lundmark, Anna K Överby
Efficient antiviral immunity requires interference with virus replication at multiple layers targeting diverse steps in the viral life cycle. Here we describe a novel flavivirus inhibition mechanism that results in interferon-mediated obstruction of tick-borne encephalitis virus particle assembly, and involves release of malfunctional membrane associated capsid (C) particles. This mechanism is controlled by the activity of the interferon-induced protein viperin, a broad spectrum antiviral interferon stimulated gene...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29046292/identification-of-ut-a1-and-aqp2-interacting-proteins-in-rat-inner-medullary-collecting-duct
#5
Chung-Lin Chou, Gloria Hwang, Daniel J Hageman, Lichy Han, Prashasti Agrawal, Trairak Pisitkun, Mark A Knepper
The urea channel UT-A1 and the water channel aquaporin-2 (AQP2) mediate vasopressin-regulated transport in the renal inner medullary collecting duct (IMCD). To identify the proteins that interact with UT-A1 and AQP2 in native rat IMCD cells, we carried out chemical cross-linking followed by detergent solubilization, immunoprecipitation, and LC-MS/MS analysis of the immunoprecipitated material. The analyses revealed 133 UT-A1-interacting proteins and 139 AQP2-interacting proteins, each identified in multiple replicates...
October 18, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/29044209/cell-penetrating-interactomic-inhibition-of-nuclear-factor-kappa-b-in-a-mouse-model-of-postoperative-cognitive-dysfunction
#6
So Yeong Cheon, Jeong Min Kim, Eun Hee Kam, Chun-Chang Ho, Eun Jung Kim, Seungsoo Chung, Ji-Hyun Jeong, Diane Da-Hyun Lee, Sang-Won Lee, Bon-Nyeo Koo
Some patients experience impaired cognitive functioning after surgery, a phenomenon referred to as postoperative cognitive dysfunction (POCD). Signs of POCD are closely associated with the development of systemic or hippocampal inflammation. However, the precise pathophysiological mechanisms of prevention/treatment options for POCD still remain unclear. After injury, the transcriptional factor nuclear factor-kappa B (NF-κB) is thought to regulate or stimulate inflammation amplification. Therefore, we designed a cell-penetrating fusion protein called nt-p65-TMD, which inhibits NF-κB p65 activation by translocating into the nucleus...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29040741/identification-of-new-protein-protein-and-protein-dna-interactions-linked-with-wood-formation-in-populus-trichocarpa
#7
H Earl Petzold, Stephen B Rigoulot, Chengsong Zhao, Bidisha Chanda, Xiaoyan Sheng, Mingzhe Zhao, Xiaoyan Jia, Allan W Dickerman, Eric P Beers, Amy M Brunner
Cellular processes, such as signal transduction and cell wall deposition, are organized by macromolecule interactions. Experimentally determined protein-protein interactions (PPIs) and protein-DNA interactions (PDIs) relevant to woody plant development are sparse. To begin to develop a Populus trichocarpa Torr. & A. Gray wood interactome, we applied the yeast-two-hybrid (Y2H) assay in different ways to enable the discovery of novel PPIs and connected networks. We first cloned open reading frames (ORFs) for 361 genes markedly upregulated in secondary xylem compared with secondary phloem and performed a binary Y2H screen with these proteins...
October 10, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29040625/rise-a-database-of-rna-interactome-from-sequencing-experiments
#8
Jing Gong, Di Shao, Kui Xu, Zhipeng Lu, Zhi John Lu, Yucheng T Yang, Qiangfeng Cliff Zhang
We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast...
October 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29039417/protein-interaction-perturbation-profiling-at-amino-acid-resolution
#9
Jonathan Woodsmith, Luise Apelt, Victoria Casado-Medrano, Ziya Özkan, Bernd Timmermann, Ulrich Stelzl
The identification of genomic variants in healthy and diseased individuals continues to rapidly outpace our ability to functionally annotate these variants. Techniques that both systematically assay the functional consequences of nucleotide-resolution variation and can scale to hundreds of genes are urgently required. We designed a sensitive yeast two-hybrid-based 'off switch' for positive selection of interaction-disruptive variants from complex genetic libraries. Combined with massively parallel programmed mutagenesis and a sequencing readout, this method enables systematic profiling of protein-interaction determinants at amino-acid resolution...
October 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/29039124/recent-progress-in-mass-spectrometry-proteomics-for-biomedical-research
#10
REVIEW
Xu Li, Wenqi Wang, Junjie Chen
Proteins are the key players in many cellular processes. Their composition, trafficking, and interactions underlie the dynamic processes of life. Furthermore, diseases are frequently accompanied by malfunction of proteins at multiple levels. Understanding how biological processes are regulated at the protein level is critically important to understanding the molecular basis for diseases and often shed light on disease prevention, diagnosis, and treatment. With rapid advances in mass spectrometry (MS) instruments and experimental methodologies, MS-based proteomics has become a reliable and essential tool for elucidating biological processes at the protein level...
October 13, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29033850/designing-dietary-recommendations-using-system-level-interactomics-analysis-and-network-based-inference
#11
Tingting Zheng, Yueqiong Ni, Jun Li, Billy K C Chow, Gianni Panagiotou
Background: A range of computational methods that rely on the analysis of genome-wide expression datasets have been developed and successfully used for drug repositioning. The success of these methods is based on the hypothesis that introducing a factor (in this case, a drug molecule) that could reverse the disease gene expression signature will lead to a therapeutic effect. However, it has also been shown that globally reversing the disease expression signature is not a prerequisite for drug activity. On the other hand, the basic idea of significant anti-correlation in expression profiles could have great value for establishing diet-disease associations and could provide new insights into the role of dietary interventions in disease...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29030113/proteomic-analyses-of-signalling-complexes-associated-with-receptor-tyrosine-kinase-identify-novel-members-of-fibroblast-growth-factor-receptor-3-interactome
#12
Lukas Balek, Pavel Nemec, Peter Konik, Michaela Kunova Bosakova, Miroslav Varecha, Iva Gudernova, Jirina Medalova, Deborah Krakow, Pavel Krejci
Receptor tyrosine kinases (RTKs) form multiprotein complexes that initiate and propagate intracellular signals and determine the RTK-specific signalling patterns. Unravelling the full complexity of protein interactions within the RTK-associated complexes is essential for understanding of RTK functions, yet it remains an understudied area of cell biology. We describe a comprehensive approach to characterize RTK interactome. A single tag immunoprecipitation and phosphotyrosine protein isolation followed by mass-spectrometry was used to identify proteins interacting with fibroblast growth factor receptor 3 (FGFR3)...
October 10, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/29028184/native-kcc2-interactome-reveals-pacsin1-as-a-critical-regulator-of-synaptic-inhibition
#13
Vivek Mahadevan, C Sahara Khademullah, Zahra Dargaei, Jonah Chevrier, Pavel Uvarov, Julian Kwan, Richard D Bagshaw, Tony Pawson, Andrew Emili, Yves De Koninck, Victor Anggono, Matti Airaksinen, Melanie A Woodin
KCC2 is a neuron-specific K(+)-Cl(-) cotransporter essential for establishing the Cl(-) gradient required for hyperpolarizing inhibition in the central nervous system (CNS). KCC2 is highly localized to excitatory synapses where it regulates spine morphogenesis and AMPA receptor confinement. Aberrant KCC2 function contributes to human neurological disorders including epilepsy and neuropathic pain. Using functional proteomics, we identified the KCC2-interactome in the mouse brain to determine KCC2-protein interactions that regulate KCC2 function...
October 13, 2017: ELife
https://www.readbyqxmd.com/read/29024215/structural-and-functional-features-of-lysine-acetylation-of-plant-and-animal-tubulins
#14
Alexey V Raevsky, Mohsen Sharifi, Dariya A Samofalova, Pavel A Karpov, Yaroslav B Blume
The study of the genome and the proteome of different species and representatives of distinct kingdoms, especially detection of proteome via wide-scaled analyses has various challenges and pitfalls. Attempts to combine all available information together and isolate some common features for determination of the pathway and their mechanism of action generally have a highly complicated nature. However, microtubule (MT) monomers are highly conserved protein structures, and microtubules are structurally conserved from Homo sapiens to Arabidopsis thaliana...
October 10, 2017: Cell Biology International
https://www.readbyqxmd.com/read/29021291/a-genome-wide-interactome-of-dna-associated-proteins-in-the-human-liver
#15
Ryne C Ramaker, Daniel Savic, Andrew A Hardigan, Kimberly Newberry, Gregory M Cooper, Richard M Myers, Sara J Cooper
Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology differ in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation...
October 11, 2017: Genome Research
https://www.readbyqxmd.com/read/29019124/native-dige-efficient-tool-to-elucidate-protein-interactomes
#16
Diksha Dani, Norbert A Dencher
Protein-protein interactions and multi-protein assemblies are inherent features of proteomes, involving soluble and membrane proteins. This imparts structural and functional heterogeneity to the proteome. One needs to consider this aspect while studying changes in abundance or activities of proteins in response to any physiological stimulus. Abundance changes in components of a given proteome can be best visualized and quantified using electrophoresis-based approaches. Here, we describe the method of Blue Native Difference Gel Electrophoresis (BN DIGE) to quantify abundance changes in proteins in the context of protein-protein interactions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29018125/more-than-enzymes-that-make-or-break-cyclic-di-gmp-local-signaling-in-the-interactome-of-ggdef-eal-domain-proteins-of-escherichia-coli
#17
Olga Sarenko, Gisela Klauck, Franziska M Wilke, Vanessa Pfiffer, Anja M Richter, Susanne Herbst, Volkhard Kaever, Regine Hengge
The bacterial second messenger bis-(3'-5')-cyclic diguanosine monophosphate (c-di-GMP) ubiquitously promotes bacterial biofilm formation. Intracellular pools of c-di-GMP seem to be dynamically negotiated by diguanylate cyclases (DGCs, with GGDEF domains) and specific phosphodiesterases (PDEs, with EAL or HD-GYP domains). Most bacterial species possess multiple DGCs and PDEs, often with surprisingly distinct and specific output functions. One explanation for such specificity is "local" c-di-GMP signaling, which is believed to involve direct interactions between specific DGC/PDE pairs and c-di-GMP-binding effector/target systems...
October 10, 2017: MBio
https://www.readbyqxmd.com/read/29016918/a-critical-view-on-abc-transporters-and-their-interacting-partners-in-auxin-transport
#18
Markus Geisler, Bibek Aryal, Martin di Donato, Pengchao Hao
Different subclasses of ATP-binding cassette (ABC) transporters have been implicated in the transport of native variants of the phytohormone auxin. Here, the putative, individual roles of key members belonging to the ABCB, ABCD and ABCG families, respectively, are highlighted and the knowledge of their assumed expression and transport routes is reviewed and compared with their mutant phenotypes. Protein-protein interactions between ABC transporters and regulatory components during auxin transport are summarized and their importance is critically discussed...
July 31, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28993251/hypoxia-ischemia-modifies-postsynaptic-glun2b-containing-nmda-receptor-complexes-in-the-neonatal-mouse-brain
#19
Fuxin Lu, Guo Shao, Yongqiang Wang, Shenheng Guan, Alma L Burlingame, Xuemei Liu, Xiao Liang, Renatta Knox, Donna M Ferriero, Xiangning Jiang
The N-methyl-d-aspartate-type glutamate receptor (NMDAR)-associated multiprotein complexes are indispensable for synaptic plasticity and cognitive functions. While purification and proteomic analyses of these signaling complexes have been performed in adult rodent and human brain, much less is known about the protein composition of NMDAR complexes in the developing brain and their modifications by neonatal hypoxic-ischemic (HI) brain injury. In this study, the postsynaptic density proteins were prepared from postnatal day 9 naïve, sham-operated and HI-injured mouse cortex...
October 6, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/28992536/how-many-receptor-like-kinases-are-required-to-operate-a-pollen-tube
#20
REVIEW
Jorge P Muschietti, Diego L Wengier
Successful fertilization depends on active molecular dialogues that the male gametophyte can establish with the pistil and the female gametophyte. Pollen grains and stigmas must recognize each other; pollen tubes need to identify the pistil tissues they will penetrate, follow positional cues to exit the transmitting tract and finally, locate the ovules. These molecular dialogues directly affect pollen tube growth rate and orientation. Receptor-like kinases (RLKs) are natural candidates for the perception and decoding of extracellular signals and their transduction to downstream cytoplasmic interactors...
October 6, 2017: Current Opinion in Plant Biology
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