52 research outputs found
Statistical mixing and aggregation in Feller diffusion
We consider Feller mean-reverting square-root diffusion, which has been
applied to model a wide variety of processes with linearly state-dependent
diffusion, such as stochastic volatility and interest rates in finance, and
neuronal and populations dynamics in natural sciences. We focus on the
statistical mixing (or superstatistical) process in which the parameter related
to the mean value can fluctuate - a plausible mechanism for the emergence of
heavy-tailed distributions. We obtain analytical results for the associated
probability density function (both stationary and time dependent), its
correlation structure and aggregation properties. Our results are applied to
explain the statistics of stock traded volume at different aggregation scales.Comment: 16 pages, 3 figures. To be published in Journal of Statistical
Mechanics: Theory and Experimen
Conditioned medium effects on reducing shear and dilution stress in plant cell cultures
[SPA] A pesar de las ventajas que presentan los cultivos de células vegetales para expresión y
producción de proteínas y otros metabolitos de interés en biorreactores frente a los
cultivos microbianos, tienen algunas limitaciones. Dos de las más importantes son el alto
porcentaje de inóculo que se necesita para que los cultivos sean viables y el estrés por
cizalla que sufren por la agitación mecánica. El estrés por dilución, o bajo porcentaje de
inóculo, y el estrés por cizalla dan lugar al proceso de muerte celular programada (MCP).
En estudios previos se ha visto que un medio de cultivo condicionado puede proteger a las
células de la MCP. En este trabajo se ha estudiado este efecto frente al estrés por cizalla y
por dilución que sufren los cultivos celulares vegetales a escala de matraz, para poder
aplicarlo a cultivos en biorreactores. [ENG] Although there are advantages about using plant cell cultures as expression system to
produce proteins and metabolites of interest in bioreactors comparing to microbial
cultures, they also have some limitations. Two of the most important ones are the high
inoculum percentage is needed to have viable cultures and the shear stress they suffer from
mechanic agitation. Both stresses lead to programming cell death (PCD). In previous
studies, it has been demonstrated that a cell-conditioned growth medium has a protective
effect against PCD. In this work, we have studied this effect against both stresses in flasks
cultures, to apply it in the future to bioreactor cultures.Este trabajo está subvencionado por el Proyecto PID2021-127933OB-C21 financiado por
MCIN/AEI/10.13039/501100011033/ y FEDER a MEC y JW, Catedra BIONET en Biotecnología y
el proyecto AGROALNEXT del Plan de Recuperación y Resiliencia. Ayuda DIN2020-011559
financiada por MCIN/AEI/ 10.13039/501100011033 y según proceda, por “FSE Invierte en tu
futuro” o por la “Unión Europea NextGenerationEU/PRTR”
pcrEfficiency: a Web tool for PCR amplification efficiency prediction
<p>Abstract</p> <p>Background</p> <p>Relative calculation of differential gene expression in quantitative PCR reactions requires comparison between amplification experiments that include reference genes and genes under study. Ignoring the differences between their efficiencies may lead to miscalculation of gene expression even with the same starting amount of template. Although there are several tools performing PCR primer design, there is no tool available that predicts PCR efficiency for a given amplicon and primer pair.</p> <p>Results</p> <p>We have used a statistical approach based on 90 primer pair combinations amplifying templates from bacteria, yeast, plants and humans, ranging in size between 74 and 907 bp to identify the parameters that affect PCR efficiency. We developed a generalized additive model fitting the data and constructed an open source Web interface that allows the obtention of oligonucleotides optimized for PCR with predicted amplification efficiencies starting from a given sequence.</p> <p>Conclusions</p> <p>pcrEfficiency provides an easy-to-use web interface allowing the prediction of PCR efficiencies prior to web lab experiments thus easing quantitative real-time PCR set-up. A web-based service as well the source code are provided freely at <url>http://srvgen.upct.es/efficiency.html</url> under the GPL v2 license.</p
Humans Share More Preferences for Floral Phenotypes With Pollinators Than With Pests.
Studies on the selection of floral traits usually consider pollinators and sometimes herbivores. However, humans also exert selection on floral traits of ornamental plants. We compared the preferences of bumblebees (Bombus terrestris), thrips (Frankliniella occidentalis), and humans for flowers of snapdragon. From a cross of two species, Antirrhinum majus and Antirrhinum linkianum, we selected four Recombinant Inbred Lines (RILs). We characterised scent emission from whole flowers and stamens, pollen content and viability, trichome density, floral shape, size and colour of floral parts. We tested the preferences of bumblebees, thrips, and humans for whole flowers, floral scent bouquets, stamen scent, and individual scent compounds. Humans and bumblebees showed preferences for parental species, whereas thrips preferred RILs. Colour and floral scent, in combination with other floral traits, seem relevant phenotypes for all organisms. Remarkably, visual traits override scent cues for bumblebees, although, scent is an important trait when bumblebees cannot see the flowers, and methyl benzoate was identified as a key attractant for them. The evolutionary trajectory of flowers is the result of multiple floral traits interacting with different organisms with different habits and modes of interaction
Архетип свобода у контексті французької політичної теорії та історії
Розглянуто сучасні підходи щодо аналізу політичної ментальності. У межах політологічного аналізу окреслено коло проблем, які потребують вирішення з використанням підходів психології. Зроблено висновок про те, що архетип “свобода” становить важливий елемент політичної ментальності французів.Modern approaches of analysis of political mentality are considered. Within the limits of political science analysis outlined circle of problems which need decision with the use of approaches of psychology. A conclusion is done that archetype freedom makes the important element of political mentality of French’s
Continuous-time modeling of cell fate determination in Arabidopsis flowers
<p>Abstract</p> <p>Background</p> <p>The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored.</p> <p>Results</p> <p>We propose an ordinary differential equation (ODE) model that describes the gene expression dynamics of a gene regulatory network that controls floral organ formation in the model plant <it>Arabidopsis thaliana</it>. In this model, the dimerization of MADS-box transcription factors is incorporated explicitly. The unknown parameters are estimated from (known) experimental expression data. The model is validated by simulation studies of known mutant plants.</p> <p>Conclusions</p> <p>The proposed model gives realistic predictions with respect to independent mutation data. A simulation study is carried out to predict the effects of a new type of mutation that has so far not been made in <it>Arabidopsis</it>, but that could be used as a severe test of the validity of the model. According to our predictions, the role of dimers is surprisingly important. Moreover, the functional loss of any dimer leads to one or more phenotypic alterations.</p
Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The current assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The Petunia lineage has experienced at least two rounds of paleohexaploidization, the older gamma hexaploidy event, which is shared with other Eudicots, and the more recent Solanaceae paleohexaploidy event that is shared with tomato and other Solanaceae species. Transcription factors that were targets of selection during the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for basic and applied research on a variety of unique biological phenomena
Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction
Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution
An everlasting pioneer: the story of Antirrhinum research
Despite the tremendous success of
Arabidopsis thaliana, no single model can
represent the vast range of form that is
seen in the ~250,000 existing species of
flowering plants (angiosperms). Here,
we consider the history and future of an
alternative angiosperm model — the
snapdragon Antirrhinum majus. We ask
what made Antirrhinum attractive to the
earliest students of variation and
inheritance, and how its use led to
landmark advances in plant genetics and
to our present understanding of plant
development. Finally, we show how the
wide diversity of Antirrhinum species,
combined with classical and molecular
genetics — the two traditional strengths
of Antirrhinum — provide an opportunity
for developmental, evolutionary and
ecological approaches. These factors
make A. majus an ideal comparative
angiosperm
Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms
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