Publications related to Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

Related publications (33)

A CTCF-dependent mechanism underlies the Hox timer relation to a segmented body plan

During gastrulation, Hox genes are activated in a timesequence that follows the order of the genes along their clusters. This property, which is observed in all animals that develop following a progressive rostral-to-caudal morphogenesis, is associated wit ...

Current Biology Ltd2024

Experimental and ab initio derivation of interface stress in nanomultilayered coatings: Application to immiscible Cu/W system with variable in-plane stress

Claudia Cancellieri, Pandula Manura Liyanage

Interface stress is a fundamental descriptor for interphase boundaries and is defined in strict relation to the interface energy. In nanomultilayers with their intrinsically high interface density, the functional properties are dictated by the interface st ...

Elsevier2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Wayo Matsushima, Didier Trono, Evaristo Jose Planet Letschert

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Succinct ordering and aggregation constraints in algebraic array theories

Viktor Kuncak, Rodrigo Raya

We discuss two extensions to a recently introduced theory of arrays, which are based on considerations coming from the model theory of power structures. First, we discuss how the ordering relation on the index set can be expressed succinctly by referring t ...

Elsevier Science Inc2024

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

Nagammal Neelagandan

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, g ...

Amer Assoc Advancement Science2024

Whole-genome doubling drives oncogenic loss of chromatin segregation

Juan Diaz Miyar, Elisa Oricchio, Natalya Katanayeva, Daniele Tavernari, Ruxandra-Andreea Lambuta

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies(1-8). However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotyp ...

NATURE PORTFOLIO2023

Shafranov shift correction to the Furth-Yoshikawa scaling of tokamak adiabatic compression

Olivier Sauter

In 1970, Furth and Yoshikawa (1970 Phys. Fluids 13 2593-6) introduced the scalings of adiabatic plasma compression. Basically, if the shape of the external plasma boundary and the aspect ratio are preserved during the compression, then the density, kinetic ...

2023

How are cells instructed to form somite boundaries by the zebrafish segmentation clock?

Olivier François Venzin

In vertebrate embryos, the elongating body axis is patterned via the sequential and rhyth-mic production of segments from a posterior unsegmented tissue called the presomitic mesoderm (PSM). This process is controlled by a population of cellular oscillator ...

EPFL2023

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Denis Duboule, Lucille Delisle, Alexandre Gauthier Aurèle Mayran, Hocine Rekaik, Célia Corinne Renée Bochaton

Temporal activation of Hox genes in mouse pseudo-embryos in vitro initiates at the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Posterior CTCF sites then successively act as transient insulators, regulating the timed tr ...

NATURE PORTFOLIO2023

Species-specific regulation of XIST by the JPX/FTX orthologs

Olga Marie Louise Rosspopoff

X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolved concom ...

OXFORD UNIV PRESS2023

Dense Image-based Predictions for Comics Analysis

Deblina Bhattacharjee

Dense image-based prediction methods have advanced tremendously in recent years. Their remarkable development has been possible due to the ample availability of real-world imagery. While these methods work well on photographs, their abilities do not genera ...

EPFL2023

Transformer Models for Vision

Jean-Baptiste Francis Marie Juliette Cordonnier

The recent developments of deep learning cover a wide variety of tasks such as image classification, text translation, playing go, and folding proteins. All these successful methods depend on a gradient-based learning algorithm to train a model on massive ...

EPFL2023

Opportunities, Challenges, and Pitfalls in Making, Characterizing, and Understanding Polymer Brushes

Harm-Anton Klok

Polymer brushes have been theoretically described, their behavior under diverse conditions has been modeled, and their preparation via surface-initiated polymerizations (SIPs) has been progressively refined. However, despite three decades of research endea ...

American Chemical Society2023

Development of a Robotic Microsurgeon for Embryonic Research

Ece Özelçi

Understanding how biological matter takes its shape is instrumental to biology, bioengineering, medicine, and bioinspired engineering. Gaining information on the principles of morphogenesis could enable clinicians to correct developmental abnormalities, ev ...

EPFL2023

Harmonic decomposition of the trace of 1D transfer matrices in layered media

Antonio Joaquin Garcia Suarez

The Transfer Matrix formalism is ubiquitous when it comes to study wave propagation in various stratified media, applications ranging from Seismology to Quantum Mechanics. A relation between variables at two points in two different layers can be establishe ...

2022

Context-dependent enhancer function revealed by targeted inter-TAD relocation

Denis Duboule, Lucille Delisle, Guillaume Andrey, Christopher Chase Bolt

Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new ne ...

Nature Portfolio2022

A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes

Linlin Cao

The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing ...

American Association of Immunologists ; Oxford University Press2022

Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications

Sebastian Maerkl, Ragunathan Bava Ganesh

Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of t ...

FRONTIERS MEDIA SA2022

Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation

Gioele La Manno, Irina Khven, Alex Russell Lederer

Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, a detailed mapping of transient cellular states during in v ...

CELL PRESS2022

Hunting for the wavefront: investigation of somite boundary positioning in zebrafish

Arianne Bercowsky Rama

Somitogenesis is the rhythmic and sequential formation of somites, which are tissue blocks that give rise to segmented adult body structures including the vertebrae and associated muscle. Somite formation is controlled by the segmentation clock, a populati ...

EPFL2022