Role of cooperative binding on noise expression

The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing transitions between discrete chemical states and the small size of biological compartments. In this paper, we propose a stochastic model for gene expression regulation including several binding sites, considering elementary reactions only. The model is used to investigate the role of cooperativity on the intrinsic fluctuations of gene expression by means of master-equation formalism. We found that the Hill coefficient and the level of noise increase as the interaction energy between activators increases. Additionally, we show that the model allows one to distinguish between two cooperative binding mechanisms.Centro Regional de Estudios GenómicosInstituto de Física La Plat

El papel morfogenético dominante de la escorrentía superficial en Licus Vallis, Marte: Resultados del análisis geomorfológico y morfométrico

Se ha analizado la cuenca de Licus Vallis, un antiguo cauce situado en la región ecuatorial de Marte, con la finalidad de evaluar el papel morfogenético que tuvo el agua superficial en su desarrollo. El análisis geomorfológico llevado a cabo en un entorno SIG ha permitido identificar numerosas morfologías fluviales relictas como canales, terrazas simétricas y un delta. Licus Vallis presenta una cuenca con rasgos propios de un relieve joven, con un perfil en desequilibrio, canales de cuarto orden, valles en V, una densidad de drenaje muy baja, y un patrón dendrítico. La erosión generada por la escorrentía superficial parece ser el proceso dominante en la formación de Licus Vallis. Sin embargo, la presencia de valles con cabecera semicircular parece indicar que la erosión asociada a surgencias pudo contribuir a la expansión por erosión remontante de los valles. Además, el hallazgo, por primera vez en este trabajo, de un posible delta de tipo Gilberten la desembocadura del sistema fluvial permitió definir el nivel de base de la cuenca y plantear la posible existencia de un antiguo mar en la región. A watershed analysis was performed to assess the morphogenetic role of surface water on the development of Licus Vallis, an ancient river valley located in the equatorial region of Mars. Terrain analysis in a GIS environment allowed the identification of numerous relict fluvial features such as channels, paired terraces and a delta. Licus Vallis has the characteristics of a young watershed with a non-equilibrium profile, fourth-order streams, V-shaped valleys, very low drainage density, and a dendritic drainage pattern. Erosion related to surface runoff appears to be the dominant process involved in the formation of Licus Vallis. Nevertheless, the presence of theatre-like valley heads seems to indicate that sapping erosion associated with springs may have played some role in the headward expansion of valleys. Moreover, the finding, for the first time in this work, of a possible Gilbert-type delta at the mouth of the fluvial system permitted to define the paleobase level of the drainage basin and suggests the existence of an ancient sea in the region

First record of Tetrastylus Ameghino, 1886 (RODENTIA; DINOMYIDAE) from the upper miocene of Uruguay

The first record for Uruguay of the dinomyid rodent Tetrastylus Ameghino, an almost complete right mandible from the upper Miocene Camacho Formation, is described. According to the p4 and m3 morphology it is inferred a juvenile-subadult ontogenetic stage for this specime

Role of cooperative binding on noise expression

The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing transitions between discrete chemical states and the small size of biological compartments. In this paper, we propose a stochastic model for gene expression regulation including several binding sites, considering elementary reactions only. The model is used to investigate the role of cooperativity on the intrinsic fluctuations of gene expression by means of master-equation formalism. We found that the Hill coefficient and the level of noise increase as the interaction energy between activators increases. Additionally, we show that the model allows one to distinguish between two cooperative binding mechanisms.Centro Regional de Estudios GenómicosInstituto de Física La Plat

Cap binding-independent recruitment of eIF4E to cytoplasmic foci

Eukaryotic translation initiation factor 4E (eIF4E) is required for cap-dependent initiation. In addition, eIF4E occurs in cytoplasmic foci such as processing bodies (PB) and stress granules (SG). We examined the role of key functional amino acid residues of eIF4E in the recruitment of this protein to cytoplasmic foci. We demonstrate that tryptophan residues required for mRNA cap recognition are not required for the recruitment of eIF4E to SG or PB. We show that a tryptophan residue required for protein-protein interactions is essential for the accumulation of eIF4E in granules. Moreover, we show, by the analysis of two Drosophila eIF4E isoforms, that the tryptophan residue is the common feature for eIF4E for the transfer of active mRNA from polysomes to other ribonucleoprotein particles in the cytoplasm. This residue resides in a putative interaction domain different than the eIF4E-BP domain. We conclude that protein-protein interactions rather than interactions with the mRNA are essential for the recruitment of eIF4E and for a putative nucleation function.Facultad de Ciencias Exacta

Cooperative binding of transcription factors promotes bimodal gene expression response

In the present work we extend and analyze the scope of our recently proposed stochastic model for transcriptional regulation, which considers an arbitrarily complex cis-regulatory system using only elementary reactions. Previously, we determined the role of cooperativity on the intrinsic fluctuations of gene expression for activating transcriptional switches, by means of master equation formalism and computer simulation. This model allowed us to distinguish between two cooperative binding mechanisms and, even though the mean expression levels were not affected differently by the acting mechanism, we showed that the associated fluctuations were different. In the present generalized model we include other regulatory functions in addition to those associated to an activator switch. Namely, we introduce repressive regulatory functions and two theoretical mechanisms that account for the biphasic response that some cis-regulatory systems show to the transcription factor concentration. We have also extended our previous master equation formalism in order to include protein production by stochastic translation of mRNA. Furthermore, we examine the graded/binary scenarios in the context of the interaction energy between transcription factors. In this sense, this is the first report to show that the cooperative binding of transcription factors to DNA promotes the "all-or-none" phenomenon observed in eukaryotic systems. In addition, we confirm that gene expression fluctuation levels associated with one of two cooperative binding mechanism never exceed the fluctuation levels of the other.Facultad de Ciencias Exacta

Detection and genome characterization of iPotato virus/i Y isolates infecting potato (iSolanum tuberosum/i L.) in La Union (Antioquia, Colombia)

Potato virus Y (PVY) is one of the most severe viruses affecting the production of potato (Solanum tuberosum) in the world. This study presents a detailed molecular analysis using nextgeneration sequencing (NGS), IC-RT-qPCR and RT-PCR on the PVY isolates infecting seed-tubers and foliage of potato plants cv. Diacol-Capiro in La Union (Antioquia, Colombia). Analysis of incidence by IC-RT-qPCR in 15 random leaf samples of three cultivation plots and fifteen sprouting tuber eye-buds reveal infection levels between 13.4 and 80%; a higher incidence of 86.7% was observed in seed-tuber samples with threshold cycle (Ct) values as low as 24.3. Genome assembly from a bulk of foliage samples resulted in a consensus PVY genome (PVY_LaUnionF) of 9,702 nt and 399 polymorphic sites within the polyprotein ORF; while the assembled genome from sprouts of tubers has 9,704 nt (PVY_LaUnionT) and contained only six polymorphic nucleotide sites. Phylogenetic analysis demonstrates that the PVY isolates from leaf samples are in the recombinant PVYNTN group (sequence identity 99%); while those from tuber sprouts are in the PVYN/NTN group with identities above 95%. Sanger sequencing of viral capsid suggests the presence of a third variant related to PVYO, a prevalent strain reported in potato fields worldwide

Localized thinning for strain concentration in suspended germanium membranes and optical method for precise thickness measurement

We deposited Ge layers on (001) Si substrates by molecular beam epitaxy and used them to fabricate suspended membranes with high uniaxial tensile strain. We demonstrate a CMOS-compatible fabrication strategy to increase strain concentration and to eliminate the Ge buffer layer near the Ge/Si hetero-interface deposited at low temperature. This is achieved by a two-steps patterning and selective etching process. First, a bridge and neck shape is patterned in the Ge membrane, then the neck is thinned from both top and bottom sides. Uniaxial tensile strain values higher than 3% were measured by Raman scattering in a Ge membrane of 76 nm thickness. For the challenging thickness measurement on micrometer-size membranes suspended far away from the substrate a characterization method based on pump-and-probe reflectivity measurements was applied, using an asynchronous optical sampling technique.EC/FP7/628197/EU/Heat Propagation and Thermal Conductivity in Nanomaterials for Nanoscale Energy Management/HEATPRONAN

Study of the Genetic Variants in BRCA1/2 and Non-BRCA Genes in a Population-Based Cohort of 2155 Breast/Ovary Cancer Patients, Including 443 Triple-Negative Breast Cancer Patients, in Argentina

Gene/s sequencing in hereditary breast/ovary cancer (HBOC) in routine diagnosis is challenged by the analysis of panels. We aim to report a retrospective analysis of BRCA1/2 and non-BRCA gene sequencing in patients with breast/ovary cancer (BOC), including triple-negative breast cancer (TNBC), in our population. In total 2155 BOC patients (1900 analyzed in BRCA1/2 and 255 by multigenic panels) gave 372 (17.2.6%) and 107 (24.1%) likely pathogenic/pathogenic variants (LPVs/PVs), including BRCA and non-BRCA genes, for the total and TNBC patients, respectively. When BOC was present in the same proband, a 51.3% rate was found for LPVs/PVs in BRCA1/2. Most of the LPVs/PVs in the panels were in BRCA1/2; non-BRCA gene LPVs/PVs were in CDH1, CHEK2, CDKN2A, MUTYH, NBN, RAD51D, and TP53. TNBC is associated with BRCA1/2 at a higher rate than the rest of the breast cancer types. The more prevalent PVs in BRCA1/2 genes (mostly in BRCA1) do not rule out the importance to panels of genes, although they are certainly far from shedding light on the gap of the 85% predicted linkage association of BOC with BRCA1/2 and are still not elucidated.Fil: Solano, Angela Rosario. Centro de Educaciones Médicas e Investigación Clínica "Norberto Quirno"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; ArgentinaFil: Mele, Pablo Gustavo. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Bioquímica Humana. Cátedra de Química Biologica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; ArgentinaFil: Jalil, Fernanda S.. Centro de Educaciones Médicas e Investigación Clínica "Norberto Quirno"; ArgentinaFil: Liria, Natalia C.. Centro de Educaciones Médicas e Investigación Clínica "Norberto Quirno"; ArgentinaFil: Podesta, Ernesto Jorge. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Bioquímica Humana. Cátedra de Química Biologica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; ArgentinaFil: Gutiérrez, Leandro G.. Centro de Educaciones Médicas e Investigación Clínica "Norberto Quirno"; Argentin

Polymorphic gallium for active resonance tuningin photonic nanostructures: from bulk gallium totwo-dimensional (2D) gallenene

Reconfigurable plasmonics is driving an extensive quest for active materials that can support a controllable modulation of their optical properties for dynamically tunable plasmonic structures. Here, polymorphic gallium (Ga) is demonstrated to be a very promising candidate for adaptive plasmonics and reconfigurable photonics applications. The Ga sp-metal is widely known as a liquid metal at room temperature. In addition to the many other compelling attributes of nanostructured Ga, including minimal oxidation and biocompatibility, its six phases have varying degrees of metallic character, providing a wide gamut of electrical conductivity and optical behavior tunability. Here, the dielectric function of the several Ga phases is introduced and correlated with their respective electronic structures. The key conditions for optimal optical modulation and switching for each Ga phase are evaluated. Additionally, we provide a comparison of Ga with other more common phase-change materials, showing better performance of Ga at optical frequencies. Furthermore, we first report, to the best of our knowledge, the optical properties of liquid Ga in the terahertz (THz) range showing its broad plasmonic tunability from ultraviolet to visible-infrared and down to the THz regime. Finally, we provide both computational and experimental evidence of extension of Ga polymorphism to bidimensional twodimensional (2D) gallenene, paving the way to new bidimensional reconfigurable plasmonic platforms.F.M. acknowledges MICINN (Spanish Ministry of Science and Innovation) through project PGC2018-096649-B-100