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(Dis)assortative partitions on random regular graphs
Abstract
We study the problem of assortative and disassortative partitions on random d -regular graphs. Nodes in the graph are partitioned into two...
Reviewing the link between language abilities and peer relations in children with developmental language disorder
BACKGROUND AND AIMS: Children with developmental language disorder (DLD) are at risk of difficulties in their friendships and peer relations. The present review explores how research directly involving children with DLD can...
Establishment and functions of DNA methylation in the germline.
Epigenetic modifications established during gametogenesis regulate transcription and other nuclear processes in gametes, but also have influences in the zygote, embryo and postnatal life. This is best understood for DNA...
Increasing incidence of immune-mediated necrotizing myopathy
Martin Klein, Heřman Mann, Lenka Pleštilová, Josef Zámečník, Zoe Betteridge, Neil McHugh, Jiří Vencovský
Aug 06, 2015
OBJECTIVES: Immune-mediated necrotizing myopathy (IMNM) is characterized by the predominant presence of necrotic muscle fibres in muscle biopsy and variable response to immunosuppressive treatment. The aims of this study were...
Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes
Florence Naillat, Heba Saadeh, Joanna Nowacka-Woszuk, Lenka Gahurova, Fatima Santos, Shin-Ichi Tomizawa, Gavin Kelsey
Jun 28, 2021
Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes.
Florence Naillat, Heba Saadeh, Joanna Nowacka-Woszuk, Lenka Gahurova, Fatima Santos, Shin-Ichi Tomizawa, Gavin Kelsey
Sep 05, 2021
BACKGROUND: Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such...
Arthritis in Idiopathic Inflammatory Myopathy
Martin Klein, Heřman Mann, Lenka Pleštilova, Zoe Betteridge, Neil McHugh, Martina Remáková, Peter Novota, Jiři Vencovsky
May 01, 2014
To determine the prevalence, distribution, and clinical manifestations of arthritis in a cohort of patients with idiopathic inflammatory myopathies (IIM). Associations with autoantibody status and HLA genetic background were...
Increasing incidence of immune-mediated necrotizing myopathy
Martin Klein, Heřman Mann, Lenka Pleštilová, Josef Zámečník, Zoe Betteridge, Neil McHugh, Jiří Vencovský
Aug 06, 2015
OBJECTIVES: Immune-mediated necrotizing myopathy (IMNM) is characterized by the predominant presence of necrotic muscle fibres in muscle biopsy and variable response to immunosuppressive treatment. The aims of this study were...
Arthritis in Idiopathic Inflammatory Myopathy
Martin Klein, Heřman Mann, Lenka Pleštilova, Zoe Betteridge, Neil McHugh, Martina Remáková, Peter Novota, Jiři Vencovsky
May 01, 2014
To determine the prevalence, distribution, and clinical manifestations of arthritis in a cohort of patients with idiopathic inflammatory myopathies (IIM). Associations with autoantibody status and HLA genetic background were...
Quantifying Drug-Induced Bone Marrow Toxicity Using a Novel Haematopoiesis Systems Pharmacology Model.
Chiara Fornari, Lenka Oplustil O'Connor, Carmen Pin, Aaron Smith, James WT Yates, SY Amy Cheung, Duncan I Jodrell, Jerome T Mettetal, Teresa A Collins
Feb 06, 2020
Haematological toxicity associated with cancer therapeutics is monitored by changes in blood cell count, and their primary effect is on proliferative progenitors in the bone marrow. Using observations in rat bone marrow and...
Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues.
Courtney W Hanna, Raquel Pérez-Palacios, Lenka Gahurova, Michael Schubert, Felix Krueger, Laura Biggins, Simon Andrews, Maria Colomé-Tatché, Deborah Bourc'his, Wendy Dean, Gavin Kelsey
Oct 28, 2020
BACKGROUND: Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically regulated by differential DNA methylation inherited from...
development Embryo Endogenous retroviruses (ERVs) Extra-embryonic Genomic Imprinting H3K27me3 Histone modifications Long terminal repeats (LTRs) Non-canonical imprinting Placenta Animals DNA Methylation Female Genomic Imprinting Histone Code Male Maternal Inheritance Mice Retroviridae Terminal Repeat Sequences
Role of co-repressor genomic landscapes in shaping the Notch response.
Stephen KK Chan, Gustavo Cerda-Moya, Robert Stojnic, Kat Millen, Bettina Fischer, Silvie Fexova, Lenka Skalska, Maria Gomez-Lamarca, Zoe Pillidge, Steven Russell, Sarah J Bray
Feb 14, 2018
Repressors are frequently deployed to limit the transcriptional response to signalling pathways. For example, several co-repressors interact directly with the DNA-binding protein CSL and are proposed to keep target genes...
Dynamic changes in histone modifications precede de novo DNA methylation in oocytes.
Kathleen R Stewart, Lenka Veselovska, Jeesun Kim, Jiahao Huang, Heba Saadeh, Shin-Ichi Tomizawa, Sébastien A Smallwood, Taiping Chen, Gavin Kelsey
Jun 24, 2019
Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly...
Engineering the protein dynamics of an ancestral luciferase.
Andrea Schenkmayerova, Gaspar P Pinto, Martin Toul, Martin Marek, Lenka Hernychova, Joan Planas-Iglesias, Veronika Daniel Liskova, Daniel Pluskal, Michal Vasina, Stephane Emond, Mark Dörr, Radka Chaloupkova, David Bednar, Zbynek Prokop, Florian Hollfelder, Uwe T Bornscheuer, Jiri Damborsky
Jul 05, 2021
Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape.
Lenka Veselovska, Sebastien A Smallwood, Heba Saadeh, Kathleen R Stewart, Felix Krueger, Stéphanie Maupetit-Méhouas, Philippe Arnaud, Shin-Ichi Tomizawa, Simon Andrews, Gavin Kelsey
Jun 24, 2019
BACKGROUND: Previously, a role was demonstrated for transcription in the acquisition of DNA methylation at imprinted control regions in oocytes. Definition of the oocyte DNA methylome by whole genome approaches revealed that the...
Animals Cell Cycle Proteins Chromatin Assembly and Disassembly CpG Islands DNA Methylation DNA Transposable Elements Female Gene Expression Profiling Genes Tumor Suppressor Genomic Imprinting High-Throughput Nucleotide Sequencing Mice Mice Transgenic Oocytes Sequence Analysis RNA Transcription Factors Transcription Initiation Site Transcriptome
Chromatin signatures at Notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation.
Lenka Skalska, Robert Stojnic, Jinghua Li, Bettina Fischer, Gustavo Cerda-Moya, Hiroshi Sakai, Shahragim Tajbakhsh, Steven Russell, Boris Adryan, Sarah J Bray
Jun 10, 2015
CBP/Nejire CSL H3K56ac Notch chromatin state Acetylation Animals Cell Cycle Proteins Chromatin DNA Intergenic DNA-Binding Proteins Drosophila Proteins Drosophila melanogaster Ecdysone Enhancer Elements Genetic Gene Expression Regulation Histone Acetyltransferases Histones Receptors Notch Repressor Proteins Transcription Factors p300-CBP Transcription Factors
Setd1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program.
David Brici, Qinyu Zhang, Susanne Reinhardt, Andreas Dahl, Hella Hartmann, Kerstin Schmidt, Neha Goveas, Jiahao Huang, Lenka Gahurova, Gavin Kelsey, Konstantinos Anastassiadis, A Francis Stewart, Andrea Kranz
Jun 24, 2019
Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases...
histone methylation MOUSE Oogenesis Pre-implantation development Transcriptional regulation Animals Blastocyst Epigenesis Genetic Female Gene Expression Profiling Gene Expression Regulation Developmental Growth Differentiation Factor 9 Histone-Lysine N-Methyltransferase Male Maternal Inheritance Mice Mice Knockout Mice Transgenic Oocytes Oogenesis RNA Messenger Single-Cell Analysis Transcription Factors Zona Pellucida Zygote
Cryptochrome 1 as a state variable of the circadian clockwork of the suprachiasmatic nucleus
David McManus, Lenka Polidarova, Nicola J Smyllie, Andrew P Patton, Johanna E Chesham, Elizabeth S Maywood, Jason W Chin, Michael H Hastings
Aug 23, 2022
The suprachiasmatic nucleus (SCN) of the hypothalamus is the principal clock driving circadian rhythms of physiology and behavior that adapt mammals to environmental cycles. Disruption of SCN-dependent rhythms compromises...
Transcription and chromatin determinants of de novo DNA methylation timing in oocytes.
Lenka Gahurova, Shin-Ichi Tomizawa, Sébastien A Smallwood, Kathleen R Stewart-Morgan, Heba Saadeh, Jeesun Kim, Simon R Andrews, Taiping Chen, Gavin Kelsey
Jun 24, 2019
BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as...
Cryptochrome proteins regulate the circadian intracellular behavior and localization of PER2 in mouse suprachiasmatic nucleus neurons.
Nicola J Smyllie, James Bagnall, Alex A Koch, Dhevahi Niranjan, Lenka Polidarova, Johanna E Chesham, Jason Chin, Carrie L Partch, Andrew SI Loudon, Michael Hastings
Jan 28, 2022
The ∼20,000 cells of the suprachiasmatic nucleus (SCN), the master circadian clock of the mammalian brain, coordinate subordinate cellular clocks across the organism, driving adaptive daily rhythms of physiology and behavior....
Cryptochrome proteins regulate the circadian intracellular behavior and localization of PER2 in mouse suprachiasmatic nucleus neurons.
Nicola J Smyllie, James Bagnall, Alex A Koch, Dhevahi Niranjan, Lenka Polidarova, Johanna E Chesham, Jason W Chin, Carrie L Partch, Andrew SI Loudon, Michael H Hastings
Feb 20, 2022
The ∼20,000 cells of the suprachiasmatic nucleus (SCN), the master circadian clock of the mammalian brain, coordinate subordinate cellular clocks across the organism, driving adaptive daily rhythms of physiology and behavior....
Engineering the protein dynamics of an ancestral luciferase.
Andrea Schenkmayerova, Gaspar P Pinto, Martin Toul, Martin Marek, Lenka Hernychova, Joan Planas-Iglesias, Veronika Daniel Liskova, Daniel Pluskal, Michal Vasina, Stephane Emond, Mark Dörr, Radka Chaloupkova, David Bednar, Zbynek Prokop, Florian Hollfelder, Uwe T Bornscheuer, Jiri Damborsky
Jul 28, 2021
Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein...
NIH 3T3 Cells Animals Mammals Mice Luciferases Luciferases Renilla Protein Engineering Enzyme Stability Temperature Mutagenesis Binding Sites Protein Conformation Kinetics Mutation Catalysis Molecular Dynamics Simulation
Published by: Nature Communications
STAT3 and TP53 mutations associate with poor prognosis in anaplastic large cell lymphoma
Cosimo Lobello, Boris Tichy, Vojtech Bystry, Lenka Radova, Daniel Filip, Marek Mraz, Ivonne-Aidee Montes-Mojarro, Nina Prokoph, Hugo Larose, Huan-Chang Liang, Geeta G. Sharma, Luca Mologni, David Belada, Katerina Kamaradova, Falko Fend, Carlo Gambacorti-Passerini, Olaf Merkel, Suzanne D. Turner, Andrea Janikova, Sarka Pospisilova
May 06, 2021
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