Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors

Nonlinear control techniques by means of a software sensor that are commonly used in chemical engineering could be also applied to genetic regulation processes. We provide here a realistic formulation of this procedure by introducing an additive white Gaussian noise, which is usually found in experimental data. Besides, we include model errors, meaning that we assume we do not know the nonlinear regulation function of the process. In order to illustrate this procedure, we employ the Goodwin dynamics of the concentrations [B.C. Goodwin, Temporal Oscillations in Cells, (Academic Press, New York, 1963)] in the simple form recently applied to single gene systems and some operon cases [H. De Jong, J. Comp. Biol. 9, 67 (2002)], which involves the dynamics of the mRNA, given protein, and metabolite concentrations. Further, we present results for a three gene case in co-regulated sets of transcription units as they occur in prokaryotes. However, instead of considering their full dynamics, we use only the data of the metabolites and a designed software sensor. We also show, more generally, that it is possible to rebuild the complete set of nonmeasured concentrations despite the uncertainties in the regulation function or, even more, in the case of not knowing the mRNA dynamics. In addition, the rebuilding of concentrations is not affected by the perturbation due to the additive white Gaussian noise and also we managed to filter the noisy output of the biological systemComment: 21 pages, 7 figures; also selected in vjbio of August 2005; this version corrects a misorder in the last three references of the published versio

A Convergent-Parallel Analysis on the Technical Assistance Provided by Information Technology Faculty Extensionists: Basis for Training and Extension Activities Plan

The study determined the satisfaction of the technical assistance conducted by faculty extensionists from a higher learning institution in Nueva Ecija, Philippines, during the academic year 2021-2022. It employed a mixed-method convergent-parallel method of study. It sought to describe the timeliness, quality of work, professionalism, courtesy, and achievement of the objectives of the technical assistance. Furthermore, it expressed the overall satisfaction of the beneficiaries with the conduct of the technical assistance using a quantitative approach. Qualitatively, using open-ended questions, the researchers analyzed the participants' responses using theme-generation techniques and identified the usefulness and impact of the technical assistance rendered to the employees and organization. The results generally revealed that the participants were satisfied with the service they received. A significant difference was seen in the level of difficulty experienced. The technical assistance provided has been practical. These participants' responses served as the basis for designing the college's training and extension development plan

G Protein-Coupled Estrogen Receptor Immunoreactivity Fluctuates During the Estrous Cycle and Show Sex Differences in the Amygdala and Dorsal Hippocampus

G protein-coupled estrogen receptor (GPER) in the amygdala and the dorsal hippocampus mediates actions of estradiol on anxiety, social recognition and spatial memory. In addition, GPER participates in the estrogenic regulation of synaptic function in the amygdala and in the process of adult neurogenesis in the dentate gyrus. While the distribution of the canonical estrogen receptors α and β in the amygdala and dorsal hippocampus are well characterized, little is known about the regional distribution of GPER in these brain regions and whether this distribution is affected by sex or the stages of the estrous cycle. In this study we performed a morphometric analysis of GPER immunoreactivity in the posterodorsal medial, anteroventral medial, basolateral, basomedial and central subdivisions of the amygdala and in all the histological layers of CA1 and the dentate gyrus of the dorsal hippocampal formation. The number of GPER immunoreactive cells was estimated in these different structures. GPER immunoreactivity was detected in all the assessed subdivisions of the amygdaloid nucleus and dorsal hippocampal formation. The number of GPER immunoreactive cells was higher in males than in estrus females in the central (P = 0.001) and the posterodorsal medial amygdala (P < 0.05); higher in males than in diestrus females in the strata orients (P < 0.01) and radiatum-lacunosum-moleculare (P < 0.05) of CA1-CA3 and in the molecular layer of the dentate gyrus (P < 0.01); higher in diestrus females than in males in the basolateral amygdala (P < 0.05); higher in diestrus females than in estrus females in the central (P < 0.01), posterodorsal medial (P < 0.01) and basolateral amygdala (P < 0.01) and higher in estrus females than in diestrus females in the strata oriens (P < 0.05) and radiatum-lacunosum-moleculare (P < 0.05) of CA1-CA3 and in the molecular layer (P < 0.05) and the hilus of the dentate gyrus (P < 0.05). The findings suggest that estrogenic regulation of the amygdala and hippocampus through GPER may be different in males and in females and may fluctuate during the estrous cycle.This study was supported by Ministero dell'Istruzione, dell'Università e della Ricerca, Italy (MIUR project Dipartimenti di Eccellenza 2018–2022) to Department of Neuroscience Rita Levi Montalcini, Agencia Estatal de Investigación, Spain (BFU2017-82754-R, PSI2017-86396-P), Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid and Fondos FEDER, GRUPOS UCM-BSCH 951579. MM fellowship was generously granted by Prof. G. C. Bergui

Methods for interpreting lists of affected genes obstained in a DNA microarray experiment

Background - The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results - Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion - It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experimen

Considering Intra-individual Genetic Heterogeneity to Understand Biodiversity

In this chapter, I am concerned with the concept of Intra-individual Genetic Hetereogeneity (IGH) and its potential influence on biodiversity estimates. Definitions of biological individuality are often indirectly dependent on genetic sampling -and vice versa. Genetic sampling typically focuses on a particular locus or set of loci, found in the the mitochondrial, chloroplast or nuclear genome. If ecological function or evolutionary individuality can be defined on the level of multiple divergent genomes, as I shall argue is the case in IGH, our current genetic sampling strategies and analytic approaches may miss out on relevant biodiversity. Now that more and more examples of IGH are available, it is becoming possible to investigate the positive and negative effects of IGH on the functioning and evolution of multicellular individuals more systematically. I consider some examples and argue that studying diversity through the lens of IGH facilitates thinking not in terms of units, but in terms of interactions between biological entities. This, in turn, enables a fresh take on the ecological and evolutionary significance of biological diversity

Sistemas ovinos de la Denominación de Origen Protegida Torta del Casar: un enfoque participativo para analizar su resiliencia

Existe unanimidad en que las tendencias económicas (asociadas a la volatilidad y aumento de precios de insumos y productos agrarios, y descenso del nivel de ingresos) son los principales retos a los que se enfrenta el sector ovino de la DOP Torta del Casar. Los ganaderos remarcan los retos institucionales, mientras que en el grupo focal remarcó los retos sociales. La adaptabilidad es la capacidad identificada como la más importante para afrontar esos retosEste trabajo ha sido cofinanciado por una beca del Gobierno de España (PRE2020-095654), el Gobierno Vasco y el proyecto RUMIRES (Proyecto PID2020-120312RA-I00 financiada por MCIN/ AEI /10.13039/501100011033). Los autores agradecen a todos los participantes en las entrevistas y el grupo focal

Synthesis of gold(I)-trifluoromethyl complexes and their role in generating spectroscopic evidence for a gold(I)-difluorocarbene species

We thank the Ghent University (IoF), the Special Research Fund (BOF) starting (SPN, CSJC) and advanced (SPN, KVH) grants and Research Foundation Flanders (FWO) (fellowship to SVB and grant to CSJC and KVH) for funding.Readily-prepared and bench-stable [Au(CF3)(NHC)] compounds were synthesized using new methodologies, starting from [Au(OH)(NHC)], [Au(Cl)(NHC)] or [Au(L)(NHC)]HF2 precursors (NHC = N-heterocyclic carbene). The mechanism of formation of these species was investigated. Consequently, a new and straightforward strategy for the mild and selective cleavage of a single carbon-fluorine bond from [Au(CF3)(NHC)] complexes was attempted and found to be reversible in the presence of an additional nucleophilic fluoride source. This straightforward technique has led to the unprecedented spectroscopic observation of a gold(I)-NHC difluorocarbene species.PostprintPeer reviewe

Reactivity of Gold Hydrides: O2 Insertion into the Au–H Bond

Dioxygen reacts with the gold(I) hydride (IPr)AuH under insertion to give the hydroperoxide, (IPr)AuOOH, a long-postulated reaction in gold catalysis and the first demonstration of O2 activation by Au-H in a well-defined system. Subsequent condensation gave the peroxide (IPr)Au-OO-Au(IPr) (IPr = 1,3-bis(2,6-diisopropylphenyl)imidazole-2-ylidene). The reaction kinetics are reported, as well as the reactivity of Au(I) hydrides with radical scavengers

Supplementary Materials for U-Th dating of carbonate crusts reveals Neanderthal origin of Iberian cave art

Materiales suplementarios al artículo de Science 2018 sobre las dataciones de arte rupestre en la Península Ibérica mediante U-TH

Highly Active and Stable Ni/La-Doped Ceria Material for Catalytic CO2Reduction by Reverse Water-Gas Shift Reaction

[EN] The design of an active, effective, and economically viable catalyst for CO2 conversion into value-added products is crucial in the fight against global warming and energy demand. We have developed very efficient catalysts for reverse water-gas shift (rWGS) reaction. Specific conditions of the synthesis by combustion allow the obtention of macroporous materials based on nanosized Ni particles supported on a mixed oxide of high purity and crystallinity. Here, we show that Ni/La-doped CeO2 catalysts─with the "right"Ni and La proportions─have an unprecedented catalytic performance per unit mass of catalyst for the rWGS reaction as the first step toward CO2 valorization. Correlations between physicochemical properties and catalytic activity, obtained using a combination of different techniques such as X-ray and neutron powder diffraction, Raman spectroscopy, in situ near ambient pressure X-ray photoelectron spectroscopy, electron microscopy, and catalytic testing, point out to optimum values for the Ni loading and the La proportion. Density functional theory calculations of elementary steps of the reaction on model Ni/ceria catalysts aid toward the microscopic understanding of the nature of the active sites. This finding offers a fundamental basis for developing economical catalysts that can be effectively used for CO2 reduction with hydrogen. A catalyst based on Ni0.07/(Ce0.9La0.1Ox)0.93 shows a CO production of 58 × 10-5 molCO·gcat-1·s-1 (700 °C, H2/CO2 = 2; selectivity to CO > 99.5), being stable for 100 h under continuous reaction.We acknowledge the financial support of the Spanish Ministry of Science and Innovation (PID2021-123287OB-I00, PID2021-122477-OB-I00, PID2021-128915NB-I00, and RTI2018-101604-B-I00) and of the CSIC through the i-LINK 2021 program (LINKA20408). Financial support has also been received from AEI-MINECO/FEDER (Nympha Project, PID2019-106315RB-I00), “Comunidad de Madrid” regional government, and the European Structural Funds (FotoArt-CM project, S2018/NMT-4367). Authors also acknowledge financial support from the grant PLEC2021-007906 funded by MCIN/AEI/10.13039/501100011033 and the “European Union NextGenerationEU/PRTR”. We are grateful to ILL (France) for making all facilities available. This project also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 832121. Computer time provided by the RES (Red Española de Supercomputación) resources at the MareNostrum 4 (BSC, Barcelona) node and the DECI resources at the BEM cluster of the WCSS based in Poland with the support from PRACE aislb is acknowledged