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Modeling Sprawling Locomotion of the Stem Amniote Orobates
The stem amnioteOrobates pabsti has been reconstructed to be capable of relatively erect, balanced, and mechanically power-saving terrestrial locomotion. This suggested that the evolution of...
Three-dimensional polygonal muscle modelling and line of action estimation in living and extinct taxa.
Oliver Demuth, Ashleigh Wiseman, Julia van Beesel, Heinrich Mallison, John R Hutchinson
Mar 01, 2022
Biomechanical models and simulations of musculoskeletal function rely on accurate muscle parameters, such as muscle masses and lines of action, to estimate force production potential and moment arms. These parameters are often...
REST-mediated recruitment of polycomb repressor complexes in mammalian cells.
Nikolaj Dietrich, Mads Lerdrup, Eskild Landt, Shuchi Agrawal-Singh, Mads Bak, Niels Tommerup, Juri Rappsilber, Erik Södersten, Klaus Hansen
May 06, 2020
Polycomb Repressive Complex (PRC) 1 and PRC2 regulate genes involved in differentiation and development. However, the mechanism for how PRC1 and PRC2 are recruited to genes in mammalian cells is unclear. Here we present evidence...
Musculoskeletal modelling of the Nile crocodile (Crocodylus niloticus) hindlimb
Ashleigh LA Wiseman, Peter J Bishop, Oliver E Demuth, Andrew R Cuff, Krijn B Michel, John R Hutchinson
Jul 28, 2021
We developed a three-dimensional, computational biomechanical model of a juvenile Nile crocodile (Crocodylus niloticus) pelvis and hindlimb, composed of 47 pelvic limb muscles, to investigate muscle function. We tested whether...
Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end.
Clinton K Lau, Francis J O'Reilly, Balaji Santhanam, Samuel E Lacey, Juri Rappsilber, Andrew P Carter
Apr 15, 2021
Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin...
Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation.
Topology-Based Three-Dimensional Reconstruction of Delicate Skeletal Fossil Remains and the Quantification of Their Taphonomic Deformation
Taphonomic and diagenetic processes inevitably distort the original skeletal morphology of fossil vertebrate remains. Key aspects of palaeobiological datasets may be directly impacted by such morphological deformation...
Three-dimensional polygonal muscle modelling and line of action estimation in living and extinct taxa.
Oliver E Demuth, Ashleigh LA Wiseman, Julia van Beesel, Heinrich Mallison, John R Hutchinson
Apr 02, 2022
Biomechanical models and simulations of musculoskeletal function rely on accurate muscle parameters, such as muscle masses and lines of action, to estimate force production potential and moment arms. These parameters are often...
TEX15 is an essential executor of MIWI2-directed transposon DNA methylation and silencing.
Theresa Schöpp, Ansgar Zoch, Rebecca V Berrens, Tania Auchynnikava, Yuka Kabayama, Lina Vasiliauskaitė, Juri Rappsilber, Robin C Allshire, Dónal O'Carroll
Jul 28, 2021
The PIWI protein MIWI2 and its associated PIWI-interacting RNAs (piRNAs) instruct DNA methylation of young active transposable elements (TEs) in the male germline. piRNAs are proposed to recruit MIWI2 to the transcriptionally...
ComplexViewer
Colin W Combe, Marine Dumousseau Sivade, Henning Hermjakob, Joshua Heimbach, Birgit HM Meldal, Gos Micklem, Sandra Orchard, Juri Rappsilber
Sep 20, 2018
SUMMARY: Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer...
Gamma secretase inhibition promotes hypoxic necrosis in mouse pancreatic ductal adenocarcinoma.
Natalie Cook, Kristopher K Frese, Tashinga E Bapiro, Michael A Jacobetz, Aarthi Gopinathan, Jodi L Miller, Sudhir S Rao, Tim Demuth, William J Howat, Duncan I Jodrell, David A Tuveson
Sep 03, 2020
Pancreatic ductal adenocarcinoma (PDA) is a highly lethal disease that is refractory to medical intervention. Notch pathway antagonism has been shown to prevent pancreatic preneoplasia progression in mouse models, but potential...
Amyloid Precursor Protein Secretases Animals Carcinoma Pancreatic Ductal Cell Line Tumor Cell Proliferation Cyclic S-Oxides Deoxycytidine Drug Synergism Drug Therapy Combination Endothelial Cells Humans Hypoxia Mice Mice Mutant Strains Necrosis Pancreatic Neoplasms Protease Inhibitors Receptors Notch Signal Transduction Thiadiazoles Translational Research Biomedical Gemcitabine
Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes.
Shirley Tremel, Yohei Ohashi, Dustin R Morado, Jessie Bertram, Olga Perisic, Laura TL Brandt, Marie-Kristin von Wrisberg, Zhuo A Chen, Sarah L Maslen, Oleksiy Kovtun, Mark Skehel, Juri Rappsilber, Kathrin Lang, Sean Munro, John AG Briggs, Roger L Williams
Mar 10, 2021
The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is...
Tungsten bronze barium neodymium titanate (Ba<sub>6-3n</sub>Nd<sub>8+2n</sub>Ti<sub>18</sub>O<sub>54</sub>) an intrinsic nanostructured material and its defect distribution
Feridoon Azough, Robert Joseph Cernik, Bernhard Schaffer, Demie Kepaptsoglou, Quentin Mathieu Ramasse, Marco Bigatti, Amir Ali, Ian MacLaren, Juri Barthel, Marco Molinari, Jakub Dominik Baran, Stephen Charles Parker, Robert Freer
Apr 18, 2016
We investigated the structure of the tungsten bronze barium neodymium titanates Ba6-3nNd8+2nTi18O54, which are exploited as microwave dielectric ceramics. They form a complex...
TEX15 is an essential executor of MIWI2-directed transposon DNA methylation and silencing
Theresa Schöpp, Ansgar Zoch, Rebecca V. Berrens, Tania Auchynnikava, Yuka Kabayama, Lina Vasiliauskaitė, Juri Rappsilber, Robin C. Allshire, Dónal O’Carroll
Jul 27, 2020
Abstract: The PIWI protein MIWI2 and its associated PIWI-interacting RNAs (piRNAs) instruct DNA methylation of young active transposable elements (TEs) in the male germline. piRNAs are proposed to recruit MIWI2 to the...
TEX15 is an essential executor of MIWI2-directed transposon DNA methylation and silencing
Theresa Schöpp, Ansgar Zoch, Rebecca V. Berrens, Tania Auchynnikava, Yuka Kabayama, Lina Vasiliauskaitė, Juri Rappsilber, Robin C. Allshire, Dónal O’Carroll
Aug 06, 2020
Abstract: The PIWI protein MIWI2 and its associated PIWI-interacting RNAs (piRNAs) instruct DNA methylation of young active transposable elements (TEs) in the male germline. piRNAs are proposed to recruit MIWI2 to the...
Tungsten bronze barium neodymium titanate (Ba<sub>6-3n</sub>Nd<sub>8+2n</sub>Ti<sub>18</sub>O<sub>54</sub>) an intrinsic nanostructured material and its defect distribution
Feridoon Azough, Robert Joseph Cernik, Bernhard Schaffer, Demie Kepaptsoglou, Quentin Mathieu Ramasse, Marco Bigatti, Amir Ali, Ian MacLaren, Juri Barthel, Marco Molinari, Jakub Dominik Baran, Stephen Charles Parker, Robert Freer
Apr 18, 2016
We investigated the structure of the tungsten bronze barium neodymium titanates Ba6-3nNd8+2nTi18O54, which are exploited as microwave dielectric ceramics. They form a complex...
Genome-wide epistasis and co-selection study using mutual information.
Johan Pensar, Santeri Puranen, Brian Arnold, Neil MacAlasdair, Juri Kuronen, Gerry Tonkin-Hill, Maiju Pesonen, Yingying Xu, Aleksi Sipola, Leonor Sánchez-Busó, John A Lees, Claire Chewapreecha, Stephen D Bentley, Simon R Harris, Julian Parkhill, Nicholas J Croucher, Jukka Corander
Aug 20, 2019
Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level covariation of alleles...
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.
Matthew P Davis, Claudia Carrieri, Harpreet K Saini, Stijn van Dongen, Tommaso Leonardi, Giovanni Bussotti, Jack M Monahan, Tania Auchynnikava, Angelo Bitetti, Juri Rappsilber, Robin C Allshire, Alena Shkumatava, Dónal O'Carroll, Anton J Enright
Nov 23, 2017
Spermatogenesis is associated with major and unique changes to chromosomes and chromatin. Here, we sought to understand the impact of these changes on spermatogenic transcriptomes. We show that long terminal repeats (LTRs) of...
endogenous retroviruses genome evolution lncRNA Spermatogenesis Transcriptome Animals DNA Transposable Elements Endogenous Retroviruses evolution Molecular Genomics Male Mice Open Reading Frames Promoter Regions Genetic RNA Long Noncoding Spermatocytes Spermatogenesis Terminal Repeat Sequences Transcription Genetic Transcriptome
A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.
Mathieu Botte, Nathan R Zaccai, Jelger Lycklama À Nijeholt, Remy Martin, Kèvin Knoops, Gabor Papai, Juan Zou, Aurélien Deniaud, Manikandan Karuppasamy, Qiyang Jiang, Abhishek Singha Roy, Klaus Schulten, Patrick Schultz, Juri Rappsilber, Giuseppe Zaccai, Imre Berger, Ian Collinson, Christiane Schaffitzel
Dec 01, 2017
The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an...
Binding Sites Cloning Molecular Cryoelectron Microscopy Escherichia coli Escherichia coli Proteins Gene Expression Genetic Vectors Membrane Transport Proteins Methanocaldococcus Models Molecular neutron diffraction Protein Binding Protein Conformation alpha-Helical Protein Conformation beta-Strand Protein Interaction Domains and Motifs Protein Transport Recombinant Proteins SEC Translocation Channels SCATTERING Small Angle Structural Homology Protein Substrate Specificity Thermus thermophilus
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