Ikerbasque

About: Ikerbasque is a other organization based out in Bilbao, Spain. It is known for research contribution in the topics: Graphene & Quantum. The organization has 713 authors who have published 7967 publications receiving 231990 citations. The organization is also known as: Basque Foundation for Science.

Structural basis of chitin oligosaccharide deacetylation.

Abstract: Cell signaling and other biological activities of chitooligosaccharides (COSs) seem to be dependent not only on the degree of polymerization, but markedly on the specific de-N-acetylation pattern. Chitin de-N-acetylases (CDAs) catalyze the hydrolysis of the acetamido group in GlcNAc residues of chitin, chitosan, and COS. A major challenge is to understand how CDAs specifically define the distribution of GlcNAc and GlcNH2 moieties in the oligomeric chain. We report the crystal structure of the Vibrio cholerae CDA in four relevant states of its catalytic cycle. The two enzyme complexes with chitobiose and chitotriose represent the first 3D structures of a CDA with its natural substrates in a productive mode for catalysis, thereby unraveling an induced-fit mechanism with a significant conformational change of a loop closing the active site. We propose that the deacetylation pattern exhibited by different CDAs is governed by critical loops that shape and differentially block accessible subsites in the binding cleft of CE4 enzymes.

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

Abstract: DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci. We hypothesized “seesaw” dynamics between H3K4me1 and H3K4me3 in the low and intermediate DNA methylation range, in which DNA methylation discriminates between enhancers and promoters, marked by H3K4me1 and H3K4me3, respectively. Low methylated regions are H3K4me3 enriched, while those with intermediate DNA methylation levels are progressively H3K4me1 enriched. Additionally, the enrichment of H3K27ac, distinguishing active from primed enhancers, follows a plateau in the lower range of the intermediate DNA methylation level, corresponding to active enhancers, and decreases linearly in the higher range of the intermediate DNA methylation. Thus, the decrease of the DNA methylation switches smoothly the state of the enhancers from a primed to an active state. We summarize these observations into a rule of thumb of one-out-of-three methylation marks: “In each genomic region only one out of these three methylation marks {DNA methylation, H3K4me1, H3K4me3} is high. If it is the DNA methylation, the region is inactive. If it is H3K4me1, the region is an enhancer, and if it is H3K4me3, the region is a promoter”. To test our model, we used available genome-wide datasets of H3K4 methyltransferases knockouts. Our analysis suggests that CXXC proteins, as readers of non-methylated CpGs would regulate the “seesaw” mechanism that focuses H3K4me3 to unmethylated sites, while being repulsed from H3K4me1 decorated enhancers and CpG island shores. Our results show that DNA methylation discriminates promoters from enhancers through H3K4me1-H3K4me3 seesaw mechanism, and suggest its possible function in the inheritance of chromatin marks after cell division. Our analyses suggest aberrant formation of promoter-like regions and ectopic transcription of hypomethylated regions of DNA. Such mechanism process can have important implications in biological process in where it has been reported abnormal DNA methylation status such as cancer and aging.

Convergence of the multimode quantum Rabi model of circuit quantum electrodynamics

Abstract: Circuit quantum electrodynamics (QED) studies the interaction of artificial atoms, open transmission lines, and electromagnetic resonators fabricated from superconducting electronics. While the theory of an artificial atom coupled to one mode of a resonator is well studied, considering multiple modes leads to divergences which are not well understood. Here, we introduce a first-principles model of a multimode resonator coupled to a Josephson junction atom. Studying the model in the absence of any cutoff, in which the coupling rate to mode number $n$ scales as $\sqrt{n}$ for $n$ up to $\ensuremath{\infty}$, we find that quantities such as the Lamb shift do not diverge due to a natural rescaling of the bare atomic parameters that arises directly from the circuit analysis. Introducing a cutoff in the coupling from a nonzero capacitance of the Josephson junction, we provide a physical interpretation of the decoupling of higher modes in the context of circuit analysis. In addition to explaining the convergence of the quantum Rabi model with no cutoff, our work also provides a useful framework for analyzing the ultrastrong coupling regime of a multimode circuit QED.

Metallic Janus and Patchy Particles

Abstract: The concepts of Janus and patchy particles are relatively new in nanoscience. Much effort has been made during recent years to devise and fabricate asymmetric particles with multiple compositions and functionalities due to their interesting properties and potential applications in a variety of fields such as catalysis, optical imaging, or drug delivery. Here, recent advances in the field of Janus particles are highlighted, focusing on nanoparticles comprising (at least) one metallic component, which is responsible for the most interesting properties of the particles. First, the main synthetic approaches are summarized, i.e., phase separation, masking, and self-assembly techniques, and then the special properties, applications, and future prospects of metallic Janus particles are described.