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

Comparative study of magnetic properties in central region of Córdoba province, Argentina

En la presente contribución se presentan resultados obtenidos de dos perfiles ubicados en localidades cercanas en la región central de la provincia de Córdoba. El objetivo del estudio fue determinar los parámetros magnéticos de los sedimentos constitutivos de los perfiles a fin de establecer una correlación entre ambos, así como efectuar una valoración de los cambios paleoambientales registrados. Ambos perfiles fueron descriptos y muestreados en detalle; en los especímenes colectados se realizaron mediciones de susceptibilidad magnética a 470 Hz y 4700 Hz, coercitividad, coercitividad de remanencia, magnetización de saturación y magnetización remanente de saturación, S-ratio, magnetización remanente anhistérica y susceptibilidad a altas temperaturas. Los resultados obtenidos permiten inferir que a pesar de encontrarse en una misma región, existen diferencias en la señal magnética, lo cual puede deberse a mayor presencia de carbonatos en uno de los perfiles, mayor retrabajo del material, diferencias en la permeabilidad, o una combinación de todas esas causas.This contribution presents results obtained from two profiles located in nearby towns in the central region of Córdoba province. The objective of the study was to determine the magnetic parameters of the sediments that constitute the profiles in order to establish a correlation between both of them, and to evaluate any record of paleoenvironmental changes. The profiles were described and sampled in detail; in the collected specimens magnetic susceptibility at 470 Hz and 4700 Hz was measured, as well as coercivity, coercivity of remanence, saturation magnetization and remanent saturation magnetization, S-ratio, anhysteric remanent magnetization and susceptibility at high temperatures. From the obtained results it is possible to infer that despite the proximity of the profiles, there are differences in their magnetic signal, which may be due to a higher content of carbonates in one of the profiles, more remobilization of the material, permeability differences, or a combination of all these causes.Fil: Rouzaut, Sabrina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Orgeira, Maria Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Geociencias Basicas, Aplicadas y Ambientales de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Geociencias Basicas, Aplicadas y Ambientales de Buenos Aires; ArgentinaFil: Tofalo, Ofelia Rita de Las Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos ; ArgentinaFil: Vasquez, Carlos Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Geociencias Basicas, Aplicadas y Ambientales de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Geociencias Basicas, Aplicadas y Ambientales de Buenos Aires; ArgentinaFil: Argüello, G. L.. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales; ArgentinaFil: Sanabria, J.. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales; ArgentinaFil: Mansilla, L.. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales; Argentin

Study of the influence of genotype and rearing method on muscle fibre characteristics in suckling goat kids

Single born male goat kids (n = 160) from eight breeds, Florida (FL), del Guadarrama (GU), Majorera (MA), Palmera (PA), Payoya (PY), Retinta (RE), Tinerfeña (TF) and Verata (VE) were involved in the present study. This study aimed to evaluate the effect of genotype and rearing method on muscle fibre populations and morphology. Two different rearing methods were used: natural suckling (NS) and milk replacer (MR). At least 300 fibres from the Semimembranosus muscle of each experimental animal were labelled as Type I or Type II using immunohistochemistry. In this study, the Type II fibres were bigger than Type I. In addition, the VE breed displayed the highest percentage of Type I fibres, and the MA, PA and TF breeds the lowest. On the contrary, the VE breed displayed the lowest percentage of Type II fibres, while the MA breed showed the highest. Goat kids from the VE, RE, GU and PY breeds displayed bigger fibres (i.e. Types I and II) than the other studied breeds. Regarding the rearing method, animals fed MR displayed more presence of Type II fibres than Type I fibres. Natural suckling animals presented bigger fibres (i.e. Types I and II) than MR goat kids

Production system and value chain in oregano (Origanum sp.) cultivation in the province of Córdoba (Argentina)

El objetivo de esta revisión fue realizar un análisis e identificación de la problemática del Sistema de Producción y de la Cadena de Valor del Orégano en la zona del Valle de Traslasierra de la Provincia de Córdoba. En la región, se cultivan ecotipos tradicionales como Criollo, Chileno II y Compacto, y nuevos como el ?Serrano Cordobés?, ?Flor Rosa? y ?Rosa Fuerte?. El Valle Traslasierra de la Provincia de Córdoba es agroecológicamente muy apto para la producción, y para incrementar la producción del cultivo de orégano se debe optimizar el manejo agronómico de los distintos ecotipos. Los estudios ecofisiológicos realizados hasta el momento en la región sugieren que los ecotipos de arquitectura erecta (Criollo) se comportan como un idiotipo más productivo que el rastrero (Compacto). Se citan por primera vez especies fitófagas de lepidópteros como Achira bifidalis (F), Rachiplusia nu (Guenée) y Spodoptera frugiperda (Smith) entre otras, además de la presencia de distintos géneros de nemátodos. Como enfermedades, se encontró la presencia de Fusarium spp y Phomopsis sp; roya y síntomas de virosis. La cadena de valor agroalimentaria se caracterizó por poseer pequeñas explotaciones que, en su mayoría, carecieron de título de propiedad, con todo lo que esto implica. Es necesario generar asociaciones activas de productores, de manera de concentrar el poder de comercialización y de organización.The aim of the present review was to analyze and identify the problems associated with the Production System and Chain Value of Oregano in the area of Traslasierra Valley, province of Córdoba. Traditional ecotypes, such as Criollo, Chileno II and Compacto, are cultivated in the region, as well as new ecotypes such as "Serrano Cordobés", "Flor Rosa" and "Rosa Fuerte". The Traslasierra Valley of Córdoba is a very suitable area for the production and for increasing the production of oregano. However, the agricultural management of the different oregano ecotypes should be optimized. Ecophysiological studies conducted to date in the region suggest that the ecotypes of erect architecture ("Criollo") behave as more productive than the creeping one ("Compacto"). Phytophagous lepidopteran species, such as Achira bifidalis (F), Rachiplusia nu (Guenée) and Spodoptera frugiperda (Smith), among others, as well as the presence of different nematode genera are mentioned for the first time. The diseases detected included Fusarium spp., Phomopsis sp, rust, and virus symptoms. The agricultural food chain value is characterized by small farms where most of the owners lacked a property title, which has adverse consequences. Active producers associations are necessary to concentrate trade and organization possibilities.Fil: Argüello, J. A.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Núñez, S. B.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Davidenco, Vanina. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Suárez, D. A.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Seisdedos, L.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Baigorria, M. C.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: la Porta, Norma Cristina. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Ruiz, G.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Yossen, Viviana Ester. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentin

Production system and value chain in oregano (Origanum sp.) cultivation in the province of Córdoba (Argentina)

El objetivo de esta revisión fue realizar un análisis e identificación de la problemática del Sistema de Producción y de la Cadena de Valor del Orégano en la zona del Valle de Traslasierra de la Provincia de Córdoba. En la región, se cultivan ecotipos tradicionales como Criollo, Chileno II y Compacto, y nuevos como el ?Serrano Cordobés?, ?Flor Rosa? y ?Rosa Fuerte?. El Valle Traslasierra de la Provincia de Córdoba es agroecológicamente muy apto para la producción, y para incrementar la producción del cultivo de orégano se debe optimizar el manejo agronómico de los distintos ecotipos. Los estudios ecofisiológicos realizados hasta el momento en la región sugieren que los ecotipos de arquitectura erecta (Criollo) se comportan como un idiotipo más productivo que el rastrero (Compacto). Se citan por primera vez especies fitófagas de lepidópteros como Achira bifidalis (F), Rachiplusia nu (Guenée) y Spodoptera frugiperda (Smith) entre otras, además de la presencia de distintos géneros de nemátodos. Como enfermedades, se encontró la presencia de Fusarium spp y Phomopsis sp; roya y síntomas de virosis. La cadena de valor agroalimentaria se caracterizó por poseer pequeñas explotaciones que, en su mayoría, carecieron de título de propiedad, con todo lo que esto implica. Es necesario generar asociaciones activas de productores, de manera de concentrar el poder de comercialización y de organización.The aim of the present review was to analyze and identify the problems associated with the Production System and Chain Value of Oregano in the area of Traslasierra Valley, province of Córdoba. Traditional ecotypes, such as Criollo, Chileno II and Compacto, are cultivated in the region, as well as new ecotypes such as "Serrano Cordobés", "Flor Rosa" and "Rosa Fuerte". The Traslasierra Valley of Córdoba is a very suitable area for the production and for increasing the production of oregano. However, the agricultural management of the different oregano ecotypes should be optimized. Ecophysiological studies conducted to date in the region suggest that the ecotypes of erect architecture ("Criollo") behave as more productive than the creeping one ("Compacto"). Phytophagous lepidopteran species, such as Achira bifidalis (F), Rachiplusia nu (Guenée) and Spodoptera frugiperda (Smith), among others, as well as the presence of different nematode genera are mentioned for the first time. The diseases detected included Fusarium spp., Phomopsis sp, rust, and virus symptoms. The agricultural food chain value is characterized by small farms where most of the owners lacked a property title, which has adverse consequences. Active producers associations are necessary to concentrate trade and organization possibilities.Fil: Argüello, J. A.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Núñez, S. B.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Davidenco, Vanina. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Suárez, D. A.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Seisdedos, L.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Baigorria, M. C.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: la Porta, Norma Cristina. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Ruiz, G.. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; ArgentinaFil: Yossen, Viviana Ester. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentin

A four-helix bundle stores copper for methane oxidation

Methane-oxidising bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase (pMMO). Certain methanotrophs are also able to switch to using the iron-containing soluble MMO (sMMO) to catalyse methane oxidation, with this switchover regulated by copper. MMOs are Nature’s primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and MMOs have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock. We have discovered and characterised a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for pMMO. Csp1 is a tetramer of 4-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realised. Cytosolic homologues of Csp1 are present in diverse bacteria thus challenging the dogma that such organisms do not use copper in this location

Hetero-cycloreversions Mediated by Photoinduced Electron Transfer

[EN] Discovered more than eight decades ago, the Diels-Alder (DA) cycloaddition (CA) remains one of the most versatile tools in synthetic organic chemistry. Hetero-DA processes are powerful methods for the synthesis of densely functionalized six-membered heterocycles, ubiquitous substructures found in natural products and bioactive compounds. These reactions frequently employ azadienes and oxadienes, but only a few groups have reported DA processes with thiadienes. The electron transfer (ET) version of the DA reaction, though less investigated, has emerged as a subject of increasing interest. In the last two decades, researchers have paid closer attention to radical ionic hetero-cycloreversions, mainly in connection with their possible involvement in the repair of pyrimidine(6-4)pyrimidone photolesions in DNA by photolyases. In biological systems, these reactions likely occur through a reductive photosensitization mechanism. In addition, photooxidation can lead to cycloreversion (CR) reactions, and researchers can exploit this strategy for DNA repair therapies. In this Account, we discuss electron-transfer (ET) mediated hetero-CR reactions. We focus on the oxidative and reductive ET splitting of oxetanes, azetidines, and thietanes. Photoinduced electron transfer facilitates the splitting of a variety of four-membered heterocycles. In this context, researchers have commonly examined oxetanes, both experimentally and theoretically. Although a few studies have reported the cycloreversion of azetidines and thietanes carried out under electron transfer conditions, the number of examples remains limited. In general, the cleavage of the ionized four-membered rings appears to occur via a nonconcerted two-step mechanism. The trapping of the intermediate 1,4-radical ions and transient absorption spectroscopy data support this hypothesis, and it explains the observed loss of stereochemistry in the products. In the initial step, either C-C or C-X bond breaking may occur, and the preferred route depends on the substitution pattern of the ring, the type of heteroatom, and various experimental conditions. To better accommodate spin and charge, C-X cleavage happens more frequently, especially in the radical anionic version of the reaction. The addition or withdrawal of a single electron provides a new complementary synthetic strategy to activate hetero-cycloreversions. Despite its potential, this strategy remains largely unexplored. However, it offers a useful method to achieve C=X/olefin metathesis or, upon ring expansion, to construct six-membered heterocyclic rings.Financial support from the Spanish Government (Grants CTQ2010-14882, SEV2012-0267, and JCI-2010-06204) and the Generalitat Valenciana (Prometeo II/2013/005) is gratefully acknowledged.Pérez Ruiz, R.; Jiménez Molero, MC.; Miranda Alonso, MÁ. (2014). Hetero-cycloreversions Mediated by Photoinduced Electron Transfer. Accounts of Chemical Research. 47(4):1359-1368. https://doi.org/10.1021/ar4003224S1359136847

Calcium and copper transport ATPases: analogies and diversities in transduction and signaling mechanisms

The calcium transport ATPase and the copper transport ATPase are members of the P-ATPase family and retain an analogous catalytic mechanism for ATP utilization, including intermediate phosphoryl transfer to a conserved aspartyl residue, vectorial displacement of bound cation, and final hydrolytic cleavage of Pi. Both ATPases undergo protein conformational changes concomitant with catalytic events. Yet, the two ATPases are prototypes of different features with regard to transduction and signaling mechanisms. The calcium ATPase resides stably on membranes delimiting cellular compartments, acquires free Ca2+ with high affinity on one side of the membrane, and releases the bound Ca2+ on the other side of the membrane to yield a high free Ca2+ gradient. These features are a basic requirement for cellular Ca2+ signaling mechanisms. On the other hand, the copper ATPase acquires copper through exchange with donor proteins, and undergoes intracellular trafficking to deliver copper to acceptor proteins. In addition to the cation transport site and the conserved aspartate undergoing catalytic phosphorylation, the copper ATPase has copper binding regulatory sites on a unique N-terminal protein extension, and has also serine residues undergoing kinase assisted phosphorylation. These additional features are involved in the mechanism of copper ATPase intracellular trafficking which is required to deliver copper to plasma membranes for extrusion, and to the trans-Golgi network for incorporation into metalloproteins. Isoform specific glyocosylation contributes to stabilization of ATP7A copper ATPase in plasma membranes

Atlantic Leatherback Migratory Paths and Temporary Residence Areas

BACKGROUND: Sea turtles are long-distance migrants with considerable behavioural plasticity in terms of migratory patterns, habitat use and foraging sites within and among populations. However, for the most widely migrating turtle, the leatherback turtle Dermochelys coriacea, studies combining data from individuals of different populations are uncommon. Such studies are however critical to better understand intra- and inter-population variability and take it into account in the implementation of conservation strategies of this critically endangered species. Here, we investigated the movements and diving behaviour of 16 Atlantic leatherback turtles from three different nesting sites and one foraging site during their post-breeding migration to assess the potential determinants of intra- and inter-population variability in migratory patterns. METHODOLOGY/PRINCIPAL FINDINGS: Using satellite-derived behavioural and oceanographic data, we show that turtles used Temporary Residence Areas (TRAs) distributed all around the Atlantic Ocean: 9 in the neritic domain and 13 in the oceanic domain. These TRAs did not share a common oceanographic determinant but on the contrary were associated with mesoscale surface oceanographic features of different types (i.e., altimetric features and/or surface chlorophyll a concentration). Conversely, turtles exhibited relatively similar horizontal and vertical behaviours when in TRAs (i.e., slow swimming velocity/sinuous path/shallow dives) suggesting foraging activity in these productive regions. Migratory paths and TRAs distribution showed interesting similarities with the trajectories of passive satellite-tracked drifters, suggesting that the general dispersion pattern of adults from the nesting sites may reflect the extent of passive dispersion initially experienced by hatchlings. CONCLUSIONS/SIGNIFICANCE: Intra- and inter-population behavioural variability may therefore be linked with initial hatchling drift scenarios and be highly influenced by environmental conditions. This high degree of behavioural plasticity in Atlantic leatherback turtles makes species-targeted conservation strategies challenging and stresses the need for a larger dataset (>100 individuals) for providing general recommendations in terms of conservation