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https://www.readbyqxmd.com/read/28422494/genetically-encoded-2-aryl-5-carboxytetrazoles-for-site-selective-protein-photo-cross-linking
#1
Yulin Tian, Marco Paolo Jacinto, Yu Zeng, Zhipeng Yu, Jun Qu, Wenshe R Liu, Qing Lin
The genetically encoded photo-cross-linkers promise to offer a temporally controlled tool to map transient and dynamic protein-protein interaction complexes in living cells. Here we report the synthesis of a panel of 2-aryl-5-carboxytetrazole-lysine analogs (ACTKs) and their site-specific incorporation into proteins via amber codon suppression in Escherichia coli and mammalian cells. Among five ACTKs investigated, N-methylpyrroletetrazole-lysine (mPyTK) was found to give robust and site-selective photo-cross-linking reactivity in E...
April 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28417191/mapping-of-estradiol-binding-sites-through-receptor-micro-autoradiography-in-the-endometrial-stroma-of-early-pregnant-mice
#2
Telma M T Zorn, Rodolfo R Favaro, Mauricio Soto-Suazo, Walter E Stumpf
Estradiol triggers key biological responses in the endometrium, which rely on the presence and levels of its cognate receptors on target cells. Employing the receptor micro-autoradiography (RMAR) technique, we aimed to provide a temporal and spatial map of the functional binding sites for estradiol in the mouse endometrial stroma during early pregnancy. Uterine samples from days 1.5 to 7.5 of pregnancy were collected 1 h after tritiated- (3H-) estradiol administration and prepared for RMAR analysis. Autoradiographic incorporation of 3H-thymidine (after 1-h pulse) was evaluated over the same gestational interval...
April 17, 2017: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/28344190/an-artificial-intelligence-approach-fit-for-trna-gene-studies-in-the-era-of-big-sequence-data
#3
Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura
Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions...
March 24, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28336542/seten-a-tool-for-systematic-identification-and-comparison-of-processes-phenotypes-and-diseases-associated-with-rna-binding-proteins-from-condition-specific-clip-seq-profiles
#4
Gungor Budak, Rajneesh Srivastava, Sarath Chandra Janga
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single nucleotide resolution in a cell, currently there are very few tools which can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps...
March 23, 2017: RNA
https://www.readbyqxmd.com/read/28318499/loss-of-function-mutations-in-lgi4-a-secreted-ligand-involved-in-schwann-cell-myelination-are-responsible-for-arthrogryposis-multiplex-congenita
#5
Shifeng Xue, Jérôme Maluenda, Florent Marguet, Mohammad Shboul, Loïc Quevarec, Carine Bonnard, Alvin Yu Jin Ng, Sumanty Tohari, Thong Teck Tan, Mung Kei Kong, Kristin G Monaghan, Megan T Cho, Carly E Siskind, Jacinda B Sampson, Carolina Tesi Rocha, Fawaz Alkazaleh, Marie Gonzales, Luc Rigonnot, Sandra Whalen, Marta Gut, Ivo Gut, Martine Bucourt, Byrappa Venkatesh, Annie Laquerrière, Bruno Reversade, Judith Melki
Arthrogryposis multiplex congenita (AMC) is a developmental condition characterized by multiple joint contractures resulting from reduced or absent fetal movements. Through genetic mapping of disease loci and whole-exome sequencing in four unrelated multiplex families presenting with severe AMC, we identified biallelic loss-of-function mutations in LGI4 (leucine-rich glioma-inactivated 4). LGI4 is a ligand secreted by Schwann cells that regulates peripheral nerve myelination via its cognate receptor ADAM22 expressed by neurons...
April 6, 2017: American Journal of Human Genetics
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
#6
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...
April 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
#7
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
#8
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
#9
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
#10
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
#11
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...
February 2017: New Phytologist
https://www.readbyqxmd.com/read/27830652/synthetic-genome-readers-target-clustered-binding-sites-across-diverse-chromatin-states
#12
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
#13
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
#14
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. To address this question, we took advantage of mutant viruses whose viral entry into cells relies on the uniquely specific interaction of an engineered gD with epidermal growth factor receptor (EGFR)...
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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