Robust identification of interactions between heat-stress responsive genes in the chicken brain using Bayesian networks and augmented expression data

Funding: This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 812777.Bayesian networks represent a useful tool to explore interactions within biological systems. The aims of this study were to identify a reduced number of genes associated with a stress condition in chickens (Gallus gallus) and to unravel their interactions by implementing a Bayesian network approach. Initially, one publicly available dataset (3 control vs 3 heat-stressed chickens) was used to identify the stress signal, represented by 25 differentially expressed genes (DEGs). The dataset was augmented by looking for the 25 DEGs in other four publicly available databases. Bayesian network algorithms were used to discover the informative relationships between the DEGs. Only ten out of the 25 DEGs displayed interactions. Four of them were Heat Shock Proteins that could be playing a key role, especially under stress conditions, where maintaining the correct functioning of the cell machinery might be crucial. One of the DEGs is an open reading frame whose function is yet unknown, highlighting the power of Bayesian networks in knowledge discovery. Identifying an initial stress signal, augmenting it by combining other databases, and finally learning the structure of Bayesian networks allowed us to find genes closely related to stress, with the possibility of further exploring the system in future studies.Peer reviewe

Practical application of a Bayesian network approach to poultry epigenetics and stress

This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 812777. We also greatly appreciate funding from the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) grants #2018-01074 and #2017-00946 to CG-B. FP appreciates funding from São Paulo Research Foundation (FAPESP, Brazil) projects #2016/20440-3 and #2018/13600-0.Background: Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide array of possibilities in Bayesian network analysis is limited. Our study aimed to apply a BN approach, while clearly laying out our analysis choices as an example for future researchers, in order to provide further insights into the relationships among epigenetic features and a stressful condition in chickens (Gallus gallus). Results: Chickens raised under control conditions (n = 22) and chickens exposed to a social isolation protocol (n = 24) were used to identify differentially methylated regions (DMRs). A total of 60 DMRs were selected by a threshold, after bioinformatic pre-processing and analysis. The treatment was included as a binary variable (control = 0; stress = 1). Thereafter, a BN approach was applied: initially, a pre-filtering test was used for identifying pairs of features that must not be included in the process of learning the structure of the network; then, the average probability values for each arc of being part of the network were calculated; and finally, the arcs that were part of the consensus network were selected. The structure of the BN consisted of 47 out of 61 features (60 DMRs and the stressful condition), displaying 43 functional relationships. The stress condition was connected to two DMRs, one of them playing a role in tight and adhesive intracellular junctions in organs such as ovary, intestine, and brain. Conclusions: We clearly explain our steps in making each analysis choice, from discrete BN models to final generation of a consensus network from multiple model averaging searches. The epigenetic BN unravelled functional relationships among the DMRs, as well as epigenetic features in close association with the stressful condition the chickens were exposed to. The DMRs interacting with the stress condition could be further explored in future studies as possible biomarkers of stress in poultry species.Publisher PDFPeer reviewe

A two-step Bayesian network approach to identify key SNPs associated to multiple phenotypic traits in four purebred laying hen lines

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [grant number 812777].When purebred laying hen chicks hatch, they remain at a rearing farm until approximately 17 weeks of age, after which they are transferred to a laying farm. Chicks or pullets are removed from the flocks during these 17 weeks if they display any rearing abnormality. The aim of this study was to investigate associations between single nucleotide polymorphisms (SNPs) and rearing success of 4 purebred White Leghorns layer lines by implementing a Bayesian network approach. Phenotypic traits and SNPs of four purebred genetic White Leghorn layer lines were available for 23,000 rearing batches obtained between 2010 and 2020. Associations between incubation traits (clutch size, embryo mortality), rearing traits (genetic line, first week mortality, rearing abnormalities, natural death, rearing success, pullet flock age, and season) and SNPs were analyzed, using a two-step Bayesian Network (BN) approach. Furthermore, the SNPs were connected to their corresponding genes, which were further explored in bioinformatics databases. BN analysis revealed a total of 28 SNPs associated with some of the traits: ten SNPs were associated with clutch size, another 10 with rearing abnormalities, a single SNP with natural death, and seven SNPs with first week mortality. Exploration via bioinformatics databases showed that one of the SNPs (ENAH) had a protein predicted network composed of 11 other proteins. The major hub of this SNP was CDC42 protein, which has a role in egg production and reproduction. The results highlight the power of BNs in knowledge discovery and how their application in complex biological systems can help getting a deeper understanding of functionality underlying genetic variation of rearing success in laying hens. Improved welfare and production might result from the identified SNPs. Selecting for these SNPs through breeding could reduce stress and increase livability during rearing.Peer reviewe

Calidad de frutos y maduración en naranjo dulce ‘Valencia Late’ [Citrus sinensis (L) Osbeck] cv Limeira, sobre diferentes portainjertos

Para responder a las exigencias de los mercados mundiales es necesario la búsqueda permanente de portainjertos que confieran calidad a los frutos y maduración anticipada. El objetivo de este trabajo fue caracterizar plantas de naranjo dulce ‘Valencia late’ injertadas sobre 17 portainjertos, según atributos de calidad de frutos y precocidad de la maduración e identificar grupos de similares características. En un diseño completamente aleatorizado con seis repeticiones, se probaron combinaciones de naranjo dulce ‘Valencia late’ con 17 portainjertos. Al momento de la cosecha se seleccionaron al azar 15 frutos y se determinaron las siguientes variables: DE, GC, PJ, SST y ATT %, también se calculó el IM. Mediante un análisis de componentes principales, gráfico biplot y análisis de la varianza multivariado se pudieron agrupar los 17 portainjertos estudiados en cuatro grupos de acuerdo con la anticipación en la maduración. El grupo que más anticipa la cosecha se caracterizó por tener frutos con altos IM y contenidos de SST y menor ATT %; el segundo presenta frutos con altos PJ y contenidos de SST y, pero también alta ATT %; el tercero contiene los frutos con los mayores GC, los menores valores de PJ, SST, ATT % y valores intermedios para IM y DE; el grupo de menor anticipación se caracterizó por frutos con mayor ATT %, menores valores de IM y DE y valores intermedios de las otras variables.In order to respond the demands of world markets, the constantly searching of rootstocks is required. The aim of this study was to characterize plants of sweet orange ‘Valencia Late’ [Citrus sinensis (L.) Osbeck] grafted on 17 rootstocks in Entre Rios, Argentina, according to fruit quality and early harvest. In a completely randomized design with six replications, combinations of sweet orange ‘Valencia Late’ with 17 rootstocks were tested. At harvest time, on 15 randomly selected fruits, following variables: equatorial diameter, rind thickness, juice percentage, soluble solids and titratable acidity were determined, and maturity index was calculated. By Principal Component Analysis, Biplot graphic, Multivariate Analysis of Variance, the 17 rootstocks studied were classified into four groups according with the early harvest. The earliest group was characterized by fruits with larger diameter, high maturity index and contents of total soluble solids and lower acidity; the second one present fruits with high percentages of juice and soluble solids content, but also higher titratable acidity; the third one contains fruits with the largest shell thicknesses, the lowest values of percentage of juice, total soluble solids and titratable acidity and intermediate values for maturity index and equatorial diameter; the last one is characterized by fruits with higher titratable acidity, lower values of index of maturity and equatorial diameter and intermediate values in other variables.Gerencia de Comunicación e Imagen Institucional, DNA SICC, INTAFil: Chabbal, Marco Daniel. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Cátedra de Fruticultura; ArgentinaFil: Gimenez, Laura Itatí. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Cátedra de Cálculo Estadística y Biometría; ArgentinaFil: Mazza, Silvia Matilde. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Cátedra de Cálculo Estadística y Biometría; ArgentinaFil: Ramirez, M.D.J. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Cátedra de Fruticultura; ArgentinaFil: Rodriguez, V.A. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Cátedra de Fruticultura; Argentin

The start of systems biology in Ukraine

The first laboratory of Systems Biology in Ukraine (IMBIG NASU) represents a track record of its scientific results. They include the pioneered development of a web-based tool for genome-wide surveys of eukaryotic promoters for the presence of transcription factors binding sites (COTRASIF); the deciphered mechanisms of the fine-tuned and balanced response of primary hepatocytes to interferon alpha levels recorded after partial hepatectomy; the elaboration of a novel method of gene regulatory network inference compatible with GRID environment and the development of a stoichiometric model of folate-related one carbon unit metabolism in human placenta and its application for the characteristics of the system’s behavior as a whole at different human pathologies.Представлено наукові здобутки першої в Україні (ІМБіГ НАН України) лабораторії системної біології. Вони включають створення веб-інструменту для всегеномного пошуку сайтів зв’язування транскрипційних факторів у промоторах евкаріотних генів; розкриття тонко збалансованого механізму відповіді первинних гепатоцитів на дію інтерферону альфа в дозі, зареєстрованій на першому етапі регенерації печінки після часткової гепатектомії; розробку нового методу інференції мережі генної регуляції для його використання в середовищі ГРІД і створення стехіометричної моделі фолатного циклу у плаценті людини для характеристики поведінки системи за різних патологічних станів.Представлены научные наработки первой в Украине (ИМБиГ НАН Украины) лаборатории системной биологии. Они включают создание веб-инструмента для всегеномного поиска сайтов связывания транскрипционных факторов в промоторах эукариотических генов; раскрытие тонко сбалансированного механизма ответа первичных гепатоцитов на действие интерферона альфа в дозе, регистрируемой в печени на раннем этапе после частичной гепатэктомии; разработку нового метода инференции сетей генной регуляции для его использования в среде ГРИД и создание модели фолатного цикла в плаценте человека для характеристики поведения системы при разных патологических состояниях

The Orbital Order Parameter in La0.95Sr0.05MnO3 probed by Electron Spin Resonance

The temperature dependence of the electron-spin resonance linewidth in La0.95Sr0.05MnO3 has been determined and analyzed in the paramagnetic regime across the orbital ordering transition. From the temperature dependence and the anisotropy of linewidth and $g$-value the orbital order can be unambiguously determined via the mixing angle of the wave functions of the $e_{\rm g}$-doublet. The linewidth shows a similar evolution with temperature as resonant x-ray scattering results

Erratum: Assessment of uncertainties in QRPA 0νββ0\nu\beta\beta-decay nuclear matrix elements [Nucl. Phys. A 766, 107 (2006)]

This is an erratum to our previously published paper.Comment: Accepted for publication in Nucl. Phys. A, see also nucl-th/050306

Neutrinoless double-beta decay and seesaw mechanism

From the standard seesaw mechanism of neutrino mass generation, which is based on the assumption that the lepton number is violated at a large (~10exp(+15) GeV) scale, follows that the neutrinoless double-beta decay is ruled by the Majorana neutrino mass mechanism. Within this notion, for the inverted neutrino-mass hierarchy we derive allowed ranges of half-lives of the neutrinoless double-beta decay for nuclei of experimental interest with different sets of nuclear matrix elements. The present-day results of the calculation of the neutrinoless double-beta decay nuclear matrix elements are briefly discussed. We argue that if neutrinoless double-beta decay will be observed in future experiments sensitive to the effective Majorana mass in the inverted mass hierarchy region, a comparison of the derived ranges with measured half-lives will allow us to probe the standard seesaw mechanism assuming that future cosmological data will establish the sum of neutrino masses to be about 0.2 eV.Comment: Some changes in sections I, II, IV, and V; two new figures; additional reference

Crystal Field and Dzyaloshinsky-Moriya Interaction in orbitally ordered La_{0.95}Sr_{0.05}MnO_3: An ESR Study

We present a comprehensive analysis of Dzyaloshinsky-Moriya interaction and crystal-field parameters using the angular dependence of the paramagnetic resonance shift and linewidth in single crystals of La_{0.95}Sr_{0.05}MnO_3 within the orthorhombic Jahn-Teller distorted phase. The Dzyaloshinsky-Moriya interaction (~ 1K) results from the tilting of the MnO_6 octahedra against each other. The crystal-field parameters D and E are found to be of comparable magnitude (~ 1K) with D ~= -E. This indicates a strong mixing of the |3z^2-r^2> and |x^2-y^2> states for the real orbital configuration.Comment: 12 pages, 6 figure

Geometry and material effects in Casimir physics - Scattering theory

We give a comprehensive presentation of methods for calculating the Casimir force to arbitrary accuracy, for any number of objects, arbitrary shapes, susceptibility functions, and separations. The technique is applicable to objects immersed in media other than vacuum, to nonzero temperatures, and to spatial arrangements in which one object is enclosed in another. Our method combines each object's classical electromagnetic scattering amplitude with universal translation matrices, which convert between the bases used to calculate scattering for each object, but are otherwise independent of the details of the individual objects. This approach, which combines methods of statistical physics and scattering theory, is well suited to analyze many diverse phenomena. We illustrate its power and versatility by a number of examples, which show how the interplay of geometry and material properties helps to understand and control Casimir forces. We also examine whether electrodynamic Casimir forces can lead to stable levitation. Neglecting permeabilities, we prove that any equilibrium position of objects subject to such forces is unstable if the permittivities of all objects are higher or lower than that of the enveloping medium; the former being the generic case for ordinary materials in vacuum.Comment: 44 pages, 11 figures, to appear in upcoming Lecture Notes in Physics volume in Casimir physic