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https://www.readbyqxmd.com/read/28105698/characterization-and-in-vivo-regulon-determination-of-an-ecf-sigma-factor-and-its-cognate-anti-sigma-factor-in-nostoc-punctiforme
#1
Nicole Bell, Jamie J Lee, Michael L Summers
Based on primary sequence comparisons and genomic context, Npun_F4153 (SigG)/Npun_F4154 (SapG) of the cyanobacterium Nostoc punctiforme were hypothesized to encode an ECF sigma factor/anti-sigma factor pair. Transcription of sigG increased in heterocysts and akinetes, and after EDTA treatment. Interaction between SigG and the predicted cytoplasmic domain of SapG was observed in vitro. A SigG-GFP translational fusion protein localized to the periphery of vegetative cells in vivo, but lost this association following heat stress...
January 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28026090/the-mesenchymal-precursor-cell-marker-antibody-stro-1-binds-to-cell-surface-heat-shock-cognate-70
#2
Stephen Fitter, Stan Gronthos, Soo Siang Ooi, Andrew C W Zannettino
Since its discovery more than 25 years ago, the STRO-1 antibody has played a fundamental role in defining the hierarchical nature of mesenchymal precursor cells (MPC) and their progeny. STRO-1 antibody binding remains a hallmark of immature pluripotent MPC. Despite the significance of STRO-1 in the MPC field, the identity of the antigen has remained elusive. Using a combination of two-dimensional gel electrophoresis, coupled with Western blotting and Tandem mass spectroscopy, we have identified the STRO-1 antigen as heat shock cognate 70 (HSC70;HSPA8)...
December 27, 2016: Stem Cells
https://www.readbyqxmd.com/read/28004095/epitope-mapping-of-mono-and-polyclonal-antibodies-by-screening-phage-displayed-random-peptide-libraries
#3
Peter Molek, Tomaž Bratkovič
Detailed knowledge of antigenic determinants is crucial when characterizing therapeutic and diagnostic antibodies, assessing vaccine effectiveness and developing epitope-based vaccines. Most epitope mapping approaches are labor intensive and costly. In this study, we evaluated panning of phage-displayed random peptide libraries against antibodies as a tool for cognate epitope identification. We used six antibodies directed to three model protein antigens as targets to show that the approach is applicable to both mono- and polyclonal antibodies...
December 2016: Acta Chimica Slovenica
https://www.readbyqxmd.com/read/27978489/structural-mutational-and-biophysical-studies-reveal-a-canonical-mode-of-molecular-recognition-between-immune-receptor-tigit-and-nectin-2
#4
Dibyendu Samanta, Haisu Guo, Rotem Rubinstein, Udupi A Ramagopal, Steven C Almo
In addition to antigen-specific stimulation of T cell receptor (TCR) by a peptide-MHC complex, the functional outcome of TCR engagement is regulated by antigen-independent costimulatory signals. Costimulatory signals are provided by an array of interactions involving activating and inhibitory receptors expressed on T cells and their cognate ligands on antigen presenting cells. T cell immunoglobulin and ITIM domain (TIGIT), a recently identified immune receptor expressed on T and NK cells, upon interaction with either of its two ligands, nectin-2 or poliovirus receptor (PVR), inhibits activation of T and NK cells...
January 2017: Molecular Immunology
https://www.readbyqxmd.com/read/27935141/evolution-of-a-multi-step-phosphorelay-signal-transduction-system-in-ensifer-recruitment-of-the-sigma-factor-rpon-and-a-novel-enhancer-binding-protein-triggers-acid-activated-gene-expression
#5
Rui Tian, Stephan Heiden, Wan A M Osman, Julie K Ardley, Euan K James, Margaret M Gollagher, Ravi Tiwari, Rekha Seshadri, Nikos C Kyrpides, Wayne G Reeve
Most Ensifer strains are comparatively acid sensitive, compromising their persistence in low pH soils. In the acid-tolerant strain Ensifer medicae WSM419, the acid-activated expression of lpiA is essential for enhancing survival in lethal acidic conditions. Here we characterise a multi-step phosphorelay signal transduction pathway consisting of TcsA, TcrA, FsrR, RpoN and its cognate enhancer-binding protein EbpA, which is required for the induction of lpiA and the downstream acvB gene. The fsrR, tcrA, tcsA and rpoN genes were constitutively expressed, whereas lpiA and acvB were strongly acid-induced...
December 9, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27935041/avrpm2-encodes-an-rnase-like-avirulence-effector-which-is-conserved-in-the-two-different-specialized-forms-of-wheat-and-rye-powdery-mildew-fungus
#6
Coraline R Praz, Salim Bourras, Fansong Zeng, Javier Sánchez-Martín, Fabrizio Menardo, Minfeng Xue, Lijun Yang, Stefan Roffler, Rainer Böni, Gerard Herren, Kaitlin E McNally, Roi Ben-David, Francis Parlange, Simone Oberhaensli, Simon Flückiger, Luisa K Schäfer, Thomas Wicker, Dazhao Yu, Beat Keller
There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race-specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3(a2/f2) that is recognized by Pm3a/f was known molecularly. We performed map-based cloning and genome-wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2...
December 9, 2016: New Phytologist
https://www.readbyqxmd.com/read/27830652/synthetic-genome-readers-target-clustered-binding-sites-across-diverse-chromatin-states
#7
Graham S Erwin, Matthew P Grieshop, Devesh Bhimsaria, Truman J Do, José A Rodríguez-Martínez, Charu Mehta, Kanika Khanna, Scott A Swanson, Ron Stewart, James A Thomson, Parameswaran Ramanathan, Aseem Z Ansari
Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to "read" specific DNA sequences. However, the impact of different chromatin states on polyamide binding in live cells remains an unresolved question that impedes their deployment in vivo. Here, we use cross-linking of small molecules to isolate chromatin coupled to sequencing to map the binding of two bioactive and structurally distinct polyamides to genomes directly within live H1 human embryonic stem cells...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27798607/nanomechanical-mapping-of-first-binding-steps-of-a-virus-to-animal-cells
#8
David Alsteens, Richard Newton, Rajib Schubert, David Martinez-Martin, Martin Delguste, Botond Roska, Daniel J Müller
Viral infection is initiated when a virus binds to cell surface receptors. Because the cell membrane is dynamic and heterogeneous, imaging living cells and simultaneously quantifying the first viral binding events is difficult. Here, we show an atomic force and confocal microscopy set-up that allows the surface receptor landscape of cells to be imaged and the virus binding events within the first millisecond of contact with the cell to be mapped at high resolution (<50 nm). We present theoretical approaches to contour the free-energy landscape of early binding events between an engineered virus and cell surface receptors...
October 31, 2016: Nature Nanotechnology
https://www.readbyqxmd.com/read/27707922/syncytial-mutations-do-not-impair-the-specificity-of-entry-and-spread-of-a-glycoprotein-d-receptor-retargeted-herpes-simplex-virus
#9
Yu Okubo, Hiroaki Uchida, Aika Wakata, Takuma Suzuki, Tomoko Shibata, Hitomi Ikeda, Miki Yamaguchi, Justus B Cohen, Joseph C Glorioso, Mitsuo Tagaya, Hirofumi Hamada, Hideaki Tahara
: Membrane fusion, which is the key process for both initial cell entry and subsequent lateral spread of herpes simplex virus (HSV), requires the four envelope glycoproteins gB, gD, gH, and gL. Syncytial mutations, predominantly mapped to the gB and gK genes, confer hyperfusogenicity on HSV and cause multinucleated giant cells, termed syncytia. Here we asked whether interaction of gD with a cognate entry receptor remains indispensable for initiating membrane fusion of syncytial strains...
December 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27670607/mechanistic-and-evolutionary-insights-from-comparative-enzymology-of-phosphomonoesterases-and-phosphodiesterases-across-the-alkaline-phosphatase-superfamily
#10
Fanny Sunden, Ishraq AlSadhan, Artem Y Lyubimov, Susanne Ressl, Helen Wiersma-Koch, Jamar Borland, Clayton L Brown, Tory A Johnson, Zorawar Singh, Daniel Herschlag
Naively one might have expected an early division between phosphate monoesterases and diesterases of the alkaline phosphatase (AP) superfamily. On the contrary, prior results and our structural and biochemical analyses of phosphate monoesterase PafA, from Chryseobacterium meningosepticum, indicate similarities to a superfamily phosphate diesterase [Xanthomonas citri nucleotide pyrophosphatase/phosphodiesterase (NPP)] and distinct differences from the three metal ion AP superfamily monoesterase, from Escherichia coli AP (EcAP)...
November 2, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27650846/reconstructed-cell-fate-regulatory-programs-in-stem-cells-reveal-hierarchies-and-key-factors-of-neurogenesis
#11
Marco-Antonio Mendoza-Parra, Valeriya Malysheva, Mohamed Ashick Mohamed Saleem, Michele Lieb, Aurelie Godel, Hinrich Gronemeyer
Cell lineages, which shape the body architecture and specify cell functions, derive from the integration of a plethora of cell intrinsic and extrinsic signals. These signals trigger a multiplicity of decisions at several levels to modulate the activity of dynamic gene regulatory networks (GRNs), which ensure both general and cell-specific functions within a given lineage, thereby establishing cell fates. Significant knowledge about these events and the involved key drivers comes from homogeneous cell differentiation models...
November 2016: Genome Research
https://www.readbyqxmd.com/read/27591323/circulating-memory-cd4-t-cells-target-conserved-epitopes-of-rhinovirus-capsid-proteins-and-respond-rapidly-to-experimental-infection-in-humans
#12
Lyndsey M Muehling, Duy T Mai, William W Kwok, Peter W Heymann, Anna Pomés, Judith A Woodfolk
Rhinovirus (RV) is a major cause of common cold and an important trigger of acute episodes of chronic lung diseases. Antigenic variation across the numerous RV strains results in frequent infections and a lack of durable cross-protection. Because the nature of human CD4(+) T cells that target RV is largely unknown, T cell epitopes of RV capsid proteins were analyzed, and cognate T cells were characterized in healthy subjects and those infected by intranasal challenge. Peptide epitopes of the RV-A16 capsid proteins VP1 and VP2 were identified by peptide/MHC class II tetramer-guided epitope mapping, validated by direct ex vivo enumeration, and interrogated using a variety of in silico methods...
October 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27519343/genome-wide-identification-of-transcriptional-start-sites-in-the-haloarchaeon-haloferax-volcanii-based-on-differential-rna-seq-drna-seq
#13
Julia Babski, Karina A Haas, Daniela Näther-Schindler, Friedhelm Pfeiffer, Konrad U Förstner, Matthias Hammelmann, Rolf Hilker, Anke Becker, Cynthia M Sharma, Anita Marchfelder, Jörg Soppa
BACKGROUND: Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcriptome analysis of archaeal species is still rather limited. Therefore, we used dRNA-Seq to characterize the primary transcriptome of the model archaeon Haloferax volcanii...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27489943/functional-modulation-of-a-g-protein-coupled-receptor-conformational-landscape-in-a-lipid-bilayer
#14
Marina Casiraghi, Marjorie Damian, Ewen Lescop, Elodie Point, Karine Moncoq, Nelly Morellet, Daniel Levy, Jacky Marie, Eric Guittet, Jean-Louis Banères, Laurent J Catoire
Mapping the conformational landscape of G protein-coupled receptors (GPCRs), and in particular how this landscape is modulated by the membrane environment, is required to gain a clear picture of how signaling proceeds. To this end, we have developed an original strategy based on solution-state nuclear magnetic resonance combined with an efficient isotope labeling scheme. This strategy was applied to a typical GPCR, the leukotriene B4 receptor BLT2, reconstituted in a lipid bilayer. Because of this, we are able to provide direct evidence that BLT2 explores a complex landscape that includes four different conformational states for the unliganded receptor...
September 7, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27380367/structural-insights-into-the-catalytic-reaction-trigger-and-inhibition-of-d-3-hydroxybutyrate-dehydrogenase
#15
Hiroki Kanazawa, Md Mominul Hoque, Masaru Tsunoda, Kaoru Suzuki, Tamotsu Yamamoto, Gota Kawai, Jiro Kondo, Akio Takénaka
D-3-Hydroxybutyrate dehydrogenase catalyzes the reversible conversion of acetoacetate and D-3-hydroxybutyrate. These ketone bodies are both energy-storage forms of acetyl-CoA. In order to clarify the structural mechanisms of the catalytic reaction with the cognate substrate D-3-hydroxybutyrate and of the inhibition of the reaction by inhibitors, the enzyme from Alcaligenes faecalis has been analyzed by X-ray crystallography in liganded states with the substrate and with two types of inhibitor: malonate and methylmalonate...
July 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27366320/digital-methodology-to-implement-the-ecouter-engagement-process
#16
Rebecca C Wilson, Oliver W Butters, Tom Clark, Joel Minion, Andrew Turner, Madeleine J Murtagh
ECOUTER (Employing COnceptUal schema for policy and Translation Engagement in Research) - French for 'to listen' - is a new stakeholder engagement method incorporating existing evidence to help participants draw upon their own knowledge of cognate issues and interact on a topic of shared concern. The results of an ECOUTER can form the basis of recommendations for research, governance, practice and/or policy. This paper describes the development of a digital methodology for the ECOUTER engagement process based on currently available mind mapping freeware software...
2016: F1000Research
https://www.readbyqxmd.com/read/27365365/diverse-alternative-back-splicing-and-alternative-splicing-landscape-of-circular-rnas
#17
Xiao-Ou Zhang, Rui Dong, Yang Zhang, Jia-Lin Zhang, Zheng Luo, Jun Zhang, Ling-Ling Chen, Li Yang
Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and/or alternative splice site selection; however, a detailed map of alternative back-splicing/splicing in circRNAs is lacking. Here, with the upgraded CIRCexplorer2 pipeline, we systematically annotated different types of alternative back-splicing and alternative splicing events in circRNAs from various cell lines...
September 2016: Genome Research
https://www.readbyqxmd.com/read/27362745/conformational-dynamics-and-the-binding-of-specific-and-nonspecific-dna-by-the-autoinhibited-transcription-factor-ets-1
#18
Geneviève Desjardins, Mark Okon, Barbara J Graves, Lawrence P McIntosh
The affinity of the Ets-1 transcription factor for DNA is autoinhibited by an intrinsically disordered serine-rich region (SRR) and a helical inhibitory module (IM) appended to its winged helix-turn-helix ETS domain. Using NMR spectroscopy, we investigated how Ets-1 recognizes specific versus nonspecific DNA, with a focus on the roles of protein dynamics and autoinhibition in these processes. Upon binding either DNA, the two marginally stable N-terminal helices of the IM predominantly unfold, but still sample partially ordered conformations...
July 26, 2016: Biochemistry
https://www.readbyqxmd.com/read/27303665/gain-of-function-mutations-in-the-toll-like-receptor-pathway-tpl2-mediated-erk1-erk2-mapk-activation-a-path-to-tumorigenesis-in-lymphoid-neoplasms
#19
Simon Rousseau, Guy Martel
Lymphoid neoplasms form a family of cancers affecting B-cells, T-cells, and NK cells. The Toll-Like Receptor (TLR) signaling adapter molecule MYD88 is the most frequently mutated gene in these neoplasms. This signaling adaptor relays signals from TLRs to downstream effector pathways such as the Nuclear Factor kappa B (NFκB) and Mitogen Activated Protein Kinase (MAPK) pathways to regulate innate immune responses. Gain-of-function mutations such as MYD88[L265P] activate downstream signaling pathways in absence of cognate ligands for TLRs, resulting in increased cellular proliferation and survival...
2016: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/27239943/the-actions-of-relaxin-on-the-human-cardiovascular-system
#20
Mohsin Sarwar, Xiao-Jun Du, Thomas B Dschietzig, Roger J Summers
The insulin-like peptide relaxin, originally identified as a hormone of pregnancy, is now known to exert a range of pleiotropic effects including vasodilatory, anti-fibrotic, angiogenic, anti-apoptotic and anti-inflammatory effects in both males and females. Relaxin produces these effects by binding to a cognate receptor RXFP1 and activating a variety of signalling pathways including cAMP, cGMP and MAPKs as well as by altering gene expression of TGF-β, MMPs, angiogenic growth factors and endothelin receptors...
May 30, 2016: British Journal of Pharmacology
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