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https://www.readbyqxmd.com/read/28448529/a-genome-wide-analysis-of-the-rna-guided-silencing-pathway-in-coffee-reveals-insights-into-its-regulatory-mechanisms
#1
Christiane Noronha Fernandes-Brum, Pâmela Marinho Rezende, Thales Henrique Cherubino Ribeiro, Raphael Ricon de Oliveira, Thaís Cunha de Sousa Cardoso, Laurence Rodrigues do Amaral, Matheus de Souza Gomes, Antonio Chalfun-Junior
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover...
2017: PloS One
https://www.readbyqxmd.com/read/28448456/upregulation-of-mirna-4776-in-influenza-virus-infected-bronchial-epithelial-cells-is-associated-with-downregulation-of-nfkbib-and-increased-viral-survival
#2
Sreekumar Othumpangat, Nicole B Bryan, Donald H Beezhold, John D Noti
Influenza A virus (IAV) infection remains a significant cause of morbidity and mortality worldwide. One key transcription factor that is activated upon IAV infection is nuclear factor Kappa B (NF-κB). NF-κB regulation involves the inhibitor proteins NF-κB inhibitor beta (NFKBIB), (also known as IκB β), which form complexes with NF-κB to sequester it in the cytoplasm. In this study, microarray data showed differential expression of several microRNAs (miRNAs) on exposure to IAV. Target scan analysis revealed that miR-4776, miR-4514 and miR-4742 potentially target NFKBIB messenger RNA (mRNA)...
April 27, 2017: Viruses
https://www.readbyqxmd.com/read/28443117/seed-biology-updates-highlights-and-new-discoveries-in-seed-dormancy-and-germination-research
#3
REVIEW
Hiroyuki Nonogaki
An understanding of the biology of seeds has been greatly advanced in recent years. The progresses, particularly in the field of seed dormancy and germination research, have been made at a remarkable speed. Some of the possible epigenetic mechanisms, including an involvement of non-coding RNA, which were predicted for DELAY OF GERMINATION1 just a few years ago, have now been demonstrated with strong molecular and genetic evidence. Imprinting, or parent-of-origin-specific gene silencing/expression, which was characterized particularly for developing seeds, was also found in imbibed seeds and suggested for dormancy mechanisms...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439830/peptide-based-isolation-of-argonaute-protein-complexes-using-ago-app
#4
Judith Hauptmann, Gunter Meister
Argonaute (Ago) proteins bind small RNAs such as microRNAs (miRNAs) or short interfering RNAs (siRNAs), which guide them to distinct mRNAs for post-transcriptional gene silencing. Mammalian miRNA-guided gene silencing pathways mainly lead to translational repression and mRNA destabilization. To facilitate these processes, Ago proteins bind members of the GW protein family, which form central interaction platforms for the recruitment of downstream effector proteins. GW proteins use tryptophane residues (W) to bind to the surface of Ago proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28434268/ubiquitin-c-terminal-hydrolase-l1-uch-l1-as-a-therapeutic-and-diagnostic-target-in-neurodegeneration-neurotrauma-and-neuro-injuries
#5
Kevin K Wang, Zhihui Yang, George Sarkis, Isabel Torres, Vijaya Raghavan
Since its discovery as a major CNS-abundant protein 25 years ago, Ubiquitin C-terminal hydrolase-L1 (UCH-L1) has emerged as an important enzyme in regulating brain protein metabolism, by coupling to the proteasome pathway of protein degradation. Areas covered: UCH-L1 is implicated in both familial and sporadic Parkinson disease and other chronic neurodegenerative diseases. Also, UCH-L1 has been recently emerging as a biofluid-based biomarker for various forms of acute neurotrauma and CNS injury. Expert opinion: The loss of UCH-L1 activity coupled with the gain of proteinopathy function are linked to neurodegeneration such as Parkinsonism and Alzheimer's disease...
April 24, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/28432596/exploiting-the-wnt-signaling-pathway-for-clinical-purposes
#6
REVIEW
Mark L Johnson, Robert R Recker
PURPOSE OF REVIEW: The goal of this paper is to evaluate critically the literature published over the past 3 years regarding the Wnt signaling pathway. The Wnt pathway was found to be involved in bone biology in 2001-2002 with the discovery of a (G171V) mutation in the lipoprotein receptor-related protein 5 (LRP5) that resulted in high bone mass and another mutation that completely inactivated Lrp5 function and resulted in osteoporosis pseudoglioma syndrome (OPPG). The molecular biology has been complex, and very interesting...
April 21, 2017: Current Osteoporosis Reports
https://www.readbyqxmd.com/read/28431241/akt-pkb-signaling-navigating-the-network
#7
REVIEW
Brendan D Manning, Alex Toker
The Ser and Thr kinase AKT, also known as protein kinase B (PKB), was discovered 25 years ago and has been the focus of tens of thousands of studies in diverse fields of biology and medicine. There have been many advances in our knowledge of the upstream regulatory inputs into AKT, key multifunctional downstream signaling nodes (GSK3, FoxO, mTORC1), which greatly expand the functional repertoire of AKT, and the complex circuitry of this dynamically branching and looping signaling network that is ubiquitous to nearly every cell in our body...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28428227/mechanisms-in-endocrinology-the-multiple-facets-of-gh-lessons-from-lifetime-untreated-isolated-gh-deficiency-due-to-ghrh-receptor-mutation
#8
Manuel Aguiar-Oliveira, Anita Ho Souza, Carla R Oliveira, Viviane C Campos, Luiz A Oliveira-Neto, Roberto Salvatori
Twenty years ago, we described a kindred of 105 individuals with isolated GH deficiency (IGHD) in Itabaianinha County, in Brazilian northeast, due to a homozygous mutation in the GH-releasing hormone receptor gene. These subjects exhibit markedly reduced GH responsiveness to stimulatory tests, and anterior pituitary hypoplasia. Serum concentrations of IGF-I, IGF binding protein type 3, and the acid-labile subunit are markedly reduced, with a lesser reduction of IGF-II. The most striking physical findings of these IGHD individuals are the proportionate short stature, doll facies, high-pitched voice, and visceral obesity with reduced fat free mass...
April 20, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28427562/cardiokines-as-modulators-of-stress-induced-cardiac-disorders
#9
Anna Planavila, Joaquim Fernández-Solà, Francesc Villarroya
Almost 30 years ago, the protein, atrial natriuretic peptide, was identified as a heart-secreted hormone that provides a peripheral signal from the myocardium that communicates to the rest of the organism to modify blood pressure and volume under conditions of heart failure. Since then, additional peripheral factors secreted by the heart, termed cardiokines, have been identified and shown to coordinate this interorgan cross talk. In addition to this interorgan communication, cardiokines also act in an autocrine/paracrine manner to play a role in intercellular communication within the myocardium...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427227/high-dose-ascorbate-and-arsenic-trioxide-selectively-kill-acute-myeloid-leukemia-and-acute-promyelocytic-leukemia-blasts-in-vitro
#10
Nélida I Noguera, Elvira Pelosi, Daniela F Angelini, Maria Liliana Piredda, Gisella Guerrera, Eleonora Piras, Luca Battistini, Lauretta Massai, Anna Berardi, Gianfranco Catalano, Laura Cicconi, Germana Castelli, Agnese D'Angiò, Luca Pasquini, Grazia Graziani, Giuseppe Fioritoni, Maria Teresa Voso, Domenico Mastrangelo, Ugo Testa, Francesco Lo-Coco
The use of high-dose ascorbate (ASC) for the treatment of human cancer has been attempted several decades ago and has been recently revived by several in vitro and in vivo studies in solid tumors. We tested the cytotoxic effects of ASC, alone or in combination with arsenic trioxide (ATO) in acute myeloid leukemia (AML) and acute promyelocytic leukemia (APL). Leukemic cell lines and primary blasts from AML and APL patients were treated with graded concentrations of ASC, alone or in association with standard concentration (1 μM) of ATO...
March 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419460/land-plants-drive-photorespiration-as-higher-electron-sink-comparative-study-of-post-illumination-transient-o2-uptake-rates-from-liverworts-to-angiosperms-through-ferns-and-gymnosperms
#11
Hitomi Hanawa, Kimitsune Ishizaki, Kana Nohira, Daisuke Takagi, Ginga Shimakawa, Takehiro Sejima, Kei-Ichiro Shaku, Amane Makino, Chikahiro Miyake
In higher plants, the electron-sink capacity of photorespiration contributes to alleviation of photoinhibition by dissipating excess energy under conditions when photosynthesis is limited. We addressed the question at what point in the evolution of photosynthetic organisms photorespiration began to function as electron sink and replaced the flavodiiron proteins which catalyze the reduction of O2 at photosystem I in cyanobacteria. Algae do not have a higher activity of photorespiration when CO2 assimilation is limited, and it can therefore not act as an electron sink...
April 17, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28418607/current-trends-in-quantitative-proteomics-an-update
#12
Huiyan Li, Jun Han, Jingxi Pan, Teng Liu, Carol E Parker, Christoph H Borchers
Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics...
April 18, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28416576/pathways-involved-in-formation-of-mammary-organoid-architecture-have-keys-to-understanding-drug-resistance-and-to-discovery-of-druggable-targets
#13
Saori Furuta, Mina J Bissell
Signals from the extracellular matrix (ECM) are received at the cell surface receptor, transmitted to the cytoskeletons, and transferred to the nucleus and chromatin for tissue- and context-specific gene expression. Cells, in return, modulate the cell shape and ECM, allowing for the maintenance of tissue homeostasis as well as for coevolution and adaptation to the environmental signals. We postulated the existence of dynamic and reciprocal interactions between the ECM and the nucleus more than three decades ago, but now these pathways have been proven experimentally thanks to the advances in imaging and cell/molecular biology techniques...
April 17, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28414106/molecular-evolution-of-the-fusion-protein-f-gene-in-human-respiratory-syncytial-virus-subgroup-b
#14
Hirokazu Kimura, Koo Nagasawa, Ryusuke Kimura, Hiroyuki Tsukagoshi, Yuki Matsushima, Kiyotaka Fujita, Eiko Hirano, Naruhiko Ishiwada, Takako Misaki, Kazunori Oishi, Makoto Kuroda, Akihide Ryo
In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes...
April 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28412328/budded-baculovirus-particles-as-a-source-of-membrane-proteins-for-radioligand-binding-assay-the-case-of-dopamine-d1-receptor
#15
Anni Allikalt, Ago Rinken
INTRODUCTION: G-protein-coupled receptors have become very important drug targets and therefore ligand binding assays for these receptors are an essential part of drug discovery. Among a variety of experimental systems, the radioligand binding assay has remained as one of the main methods in this field for decades. Usually cell membranes or tissues are used in these experiments, however in this article we demonstrate that baculoviruses produced in Sf9 cells display recombinant receptors on their surface and therefore can be used in radioligand binding assay...
April 12, 2017: Journal of Pharmacological and Toxicological Methods
https://www.readbyqxmd.com/read/28409196/evolutionary-analysis-of-the-mammalian-tuftelin-sequence-reveals-features-of-functional-importance
#16
S Delgado, D Deutsch, J Y Sire
Tuftelin (TUFT1) is an acidic, phosphorylated glycoprotein, initially discovered in developing enamel matrix. TUFT1 is expressed in many mineralized and non-mineralized tissues. We performed an evolutionary analysis of 82 mammalian TUFT1 sequences to identify residues and motifs that were conserved during 220 million years (Ma) of evolution. We showed that 168 residues (out of the 390 residues composing the human TUFT1 sequence) are under purifying selection. Our analyses identified several, new, putatively functional domains and confirmed previously described functional domains, such as the TIP39 interaction domain, which correlates with nuclear localization of the TUFT1 protein, that was demonstrated in several tissues...
April 13, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28408977/mitogenomes-of-giant-skipper-butterflies-reveal-an-ancient-split-between-deep-and-shallow-root-feeders
#17
Jing Zhang, Qian Cong, Xiao-Ling Fan, Rongjiang Wang, Min Wang, Nick V Grishin
Background: Giant-Skipper butterflies from the genus Megathymus are North American endemics. These large and thick-bodied Skippers resemble moths and are unique in their life cycles. Grub-like at the later stages of development, caterpillars of these species feed and live inside yucca roots. Adults do not feed and are mostly local, not straying far from the patches of yucca plants. Methods: Pieces of muscle were dissected from the thorax of specimens and genomic DNA was extracted (also from the abdomen of a specimen collected nearly 60 years ago)...
2017: F1000Research
https://www.readbyqxmd.com/read/28408493/bio-zombie-the-rise-of-pseudoenzymes-in-biology
#18
James M Murphy, Hesso Farhan, Patrick A Eyers
Pseudoenzymes are catalytically dead counterparts of enzymes. Despite their first description some 50 years ago, the importance and functional diversity of these 'fit-for-purpose' polypeptides is only now being appreciated. Pseudoenzymes have been identified throughout all the kingdoms of life and, owing to predicted deficits in enzyme activity due to the absence of catalytic residues, have been variously referred to as pseudoenzymes, non-enzymes, dead enzymes, prozymes or 'zombie' proteins. An important goal of the recent Biochemical Society Pseudoenzymes-focused meeting was to explore the functional and evolutionary diversity of pseudoenzymes and to begin to evaluate their functions in biology, including cell signalling and metabolism...
April 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28408410/decreased-cohesin-in-the-brain-leads-to-defective-synapse-development-and-anxiety-related-behavior
#19
Yuki Fujita, Koji Masuda, Masashige Bando, Ryuichiro Nakato, Yuki Katou, Takashi Tanaka, Masahiro Nakayama, Keizo Takao, Tsuyoshi Miyakawa, Tatsunori Tanaka, Yukio Ago, Hitoshi Hashimoto, Katsuhiko Shirahige, Toshihide Yamashita
Abnormal epigenetic regulation can cause the nervous system to develop abnormally. Here, we sought to understand the mechanism by which this occurs by investigating the protein complex cohesin, which is considered to regulate gene expression and, when defective, is associated with higher-level brain dysfunction and the developmental disorder Cornelia de Lange syndrome (CdLS). We generated conditional Smc3-knockout mice and observed greater dendritic complexity and larger numbers of immature synapses in the cerebral cortex of Smc3(+/-) mice...
April 13, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28406627/diindolylmethane-derivatives-potent-agonists-of-the-immunostimulatory-orphan-g-protein-coupled-receptor-gpr84
#20
Thanigaimalai Pillaiyar, Meryem Köse, Katharina Sylvester, Heike Weighardt, Dominik Thimm, Gleice Borges, Irmgard Förster, Ivar von Kügelgen, Christa E Müller
The Gi protein-coupled receptor GPR84, which is activated by (hydroxy)fatty acids, is highly expressed on immune cells. Recently 3,3'-diindolylmethane was identified as a heterocyclic, non-lipid-like GPR84 agonist. We synthesized a broad range of diindolylmethane derivatives by condensation of indoles with formaldehyde in water under microwave irradiation. The products were evaluated at the human GPR84 in cAMP and β-arrestin assays. Structure-activity relationships (SARs) were steep. 3,3'-Diindolylmethanes bearing small lipophilic residues at the 5- and/or 7-position of the indole rings displayed the highest activity in cAMP assays, the most potent agonists being di-(5-fluoro-1H-indole-3-yl)methane (38, PSB-15160, EC50 80...
April 13, 2017: Journal of Medicinal Chemistry
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