Sistemas híbridos basados en grafeno y MoS2-2D para detección óptica

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Física de Materiales. Fecha de Lectura: 02-12-202

Widespread inter-individual gene expression variability in Arabidopsis thaliana.

A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform, and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about inter-individual transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24-h time course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses, with different classes of genes variable between the day and night. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants

Raman and Fluorescence Enhancement Approaches in Graphene-Based Platforms for Optical Sensing and Imaging

This article belongs to the Special Issue Physics and Chemistry of Graphene: From Fundamentals to Applications.The search for novel platforms and metamaterials for the enhancement of optical and particularly Raman signals is still an objective since optical techniques offer affordable, noninvasive methods with high spatial resolution and penetration depth adequate to detect and image a large variety of systems, from 2D materials to molecules in complex media and tissues. Definitely, plasmonic materials produce the most efficient enhancement through the surface-enhanced Raman scattering (SERS) process, allowing single-molecule detection, and are the most studied ones. Here we focus on less explored aspects of SERS such as the role of the inter-nanoparticle (NP) distance and the ultra-small NP size limit (down to a few nm) and on novel approaches involving graphene and graphene-related materials. The issues on reproducibility and homogeneity for the quantification of the probe molecules will also be discussed. Other light enhancement mechanisms, in particular resonant and interference Raman scatterings, as well as the platforms that allow combining several of them, are presented in this review with a special focus on the possibilities that graphene offers for the design and fabrication of novel architectures. Recent fluorescence enhancement platforms and strategies, so important for bio-detection and imaging, are reviewed as well as the relevance of graphene oxide and graphene/carbon nanodots in the field.The research leading to these results has received funding from Ministerio de Ciencia e Innovación (RTI2018-096918-B-C41). S.C. acknowledges the grant BES-2016-076440 from MINECO

Co-expression Networks From Gene Expression Variability Between Genetically Identical Seedlings Can Reveal Novel Regulatory Relationships.

Co-expression networks are a powerful tool to understand gene regulation. They have been used to identify new regulation and function of genes involved in plant development and their response to the environment. Up to now, co-expression networks have been inferred using transcriptomes generated on plants experiencing genetic or environmental perturbation, or from expression time series. We propose a new approach by showing that co-expression networks can be constructed in the absence of genetic and environmental perturbation, for plants at the same developmental stage. For this, we used transcriptomes that were generated from genetically identical individual plants that were grown under the same conditions and for the same amount of time. Twelve time points were used to cover the 24-h light/dark cycle. We used variability in gene expression between individual plants of the same time point to infer a co-expression network. We show that this network is biologically relevant and use it to suggest new gene functions and to identify new targets for the transcriptional regulators GI, PIF4, and PRR5. Moreover, we find different co-regulation in this network based on changes in expression between individual plants, compared to the usual approach requiring environmental perturbation. Our work shows that gene co-expression networks can be identified using variability in gene expression between individual plants, without the need for genetic or environmental perturbations. It will allow further exploration of gene regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild

Molecular mechanism of cytokinin-activated cell division in Arabidopsis

Mitogens trigger cell division in animals. In plants, cytokinins, a group of phytohormones derived from adenine, stimulate cell proliferation. Cytokinin signalling is initiated by membrane-associated histidine kinase receptors and transduced through a phosphorelay system. Here we show, in the Arabidopsis shoot apical meristem (SAM), that cytokinin regulates cell division by promoting nuclear shuttling of Myb-domain protein 3R4 (MYB3R4), a transcription factor that activates mitotic gene expression. Newly synthesized MYB3R4 protein resides predominantly in the cytoplasm. At the G2/M transition, rapid nuclear accumulation of MYB3R4—consistent with an associated transient peak in cytokinin concentration—feeds a positive-feedback loop involving importins, and initiates a transcriptional cascade that drives mitosis and cytokinesis. An engineered nuclear-restricted MYB3R4 mimics the cytokinin effects in enhancement of cell proliferation and meristem growth.Gatsby Charitable Foundatio

Extensive Natural Epigenetic Variation At A De Novo Originated Gene.

Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5'end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.9e100343

Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit.

Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment

Grain selective Cu oxidation and anomalous shift of graphene 2D Raman peak in the graphene-Cu system

Understanding the interaction between graphene and its supporting substrate is of paramount importance for the development of graphene based applications. In this work the interplay of the technologically relevant graphene-Cu system is investigated in detail as a function of substrate grain orientation in Cu polycrystalline foils. While (100) and (111) Cu grains show the well-known graphene-enhanced oxidation, (110) grains present a superior oxidation resistance compared to uncovered Cu and an anomalous shift of its graphene 2D Raman band which cannot be explained by the known effects of strain and doping. These results are interpreted in terms of a weak graphene-Cu coupling at the (110) grains, and show that graphene can actually be used as anticorrosion coating, contrary to previously reported. The anomalous shift is suggested to be the result of an enhanced outer Raman scattering process which surpasses the usually dominant inner process. Since Raman spectroscopy is widely used as first and main characterization tool of graphene, the existence of an anomalous shift on its 2D band not only challenges the current theory of Raman scattering in graphene, but also has profound implications from an experimental point of view

Raman amplification in the ultra-small limit of Ag nanoparticles on SiO2 and graphene: Size and inter-particle distance effects

Size, shape and hot spots are crucial to optimize Raman amplification from metallic nanoparticle (NPs). The amplification from radius = 1.8 ± 0.4 nm ultra-small silver NPs was explored. Increasing NP density redshifts and widens their plasmon that, according to simulations for NPs arrays, is originated by the reduction of the interparticle distance, d, becoming remarkable for d ≤ R. Inter-particle interaction red-shifts (>130 nm) and widens (>90 nm) the standard plasmon of non-interacting spherical particles. Graphene partly delocalizes the carriers enhancing the NIR spectral weight. Raman amplification of graphene phonons is moderate and depends smoothly on d while that of Rhodamine 6G (R6G) varies almost exponentially due to their location at hot-spots that depend strongly on d. The experimental correlation between amplification and plasmon position is well reproduced by simulations. The amplification originated by the ultra-small NPs is compared to that of larger particles, granular silver films with 7 < R < 15 nm grains, with similar extinction values. The amplification is found to be larger for the 1.8 nm NPs due to the higher surface/volume ration that allows higher density of hot spots. It is demonstrated that Raman amplification can be efficiently increased by depositing low density layers of ultra-small NPs on top of granular films.The research leading to these results has received funding from Ministerio de Ciencia, Innovación y Universidades (RTI2018-096918-B-C41). S.C. acknowledges the grant BES-2016-076440 from MINECO. L.M. acknowledges the European Union (grant number ERC-2013-SyG 610256 NANOCOSMOS)