Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.

Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal transduction to the core of regulation to modify expression of the affected set of target genes, and ends with an adequate response. We refer to these units as genetic sensory response units, or geSorgans.

The inclusion of geSorgans will bring a dramatic change and expansion of RegulonDB, due to the fact that we will be adding several new types of reactions and interactions. We started to collect data about signal transduction of the sigma factors, the two-component systems, of some transcription factors involved in carbon source utilization, and of genes involved in the synthesis of amino acids. We plan a high-level curation with super-pathways summarizing concatenated sets of reactions linked to those other databases that curate such information, while enabling with RegulonDB a compilation of complete geSorgans.

In addition, the number of DNA binding sites for some transcription factors has grown considerably, and therefore we decided to review systematically those sites whose lengths ranging from 40 to 60 bp with orientation and consensus sequences that are not easy to identify. The current version of RegulonDB is the beginning of a higher-level curation of gene regulation information, and eventually our database will include all regulatory mechanisms and their regulated genes. 
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Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.

Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal transduction to the core of regulation to modify expression of the affected set of target genes, and ends with an adequate response. We refer to these units as genetic sensory response units, or Gensor Units.

The inclusion of Gensor Units will bring a dramatic change and expansion of RegulonDB, due to the fact that we will be adding several new types of reactions and interactions. We started to collect data about signal transduction of the sigma factors, the two-component systems, of some transcription factors involved in carbon source utilization, and of genes involved in the synthesis of amino acids. We plan a high-level curation with super-pathways summarizing concatenated sets of reactions linked to those other databases that curate such information, while enabling with RegulonDB a compilation of complete Gensor Units.

In addition, the number of DNA binding sites for some transcription factors has grown considerably, and therefore we decided to review systematically those sites whose lengths ranging from 40 to 60 bp with orientation and consensus sequences that are not easy to identify. The current version of RegulonDB is the beginning of a higher-level curation of gene regulation information, and eventually our database will include all regulatory mechanisms and their regulated genes. 
&#xa

Análisis químicos no destructivos sobre cinco mangos de marfil de Época Ibérica

Presentamos los análisis químicos realizados sobre un conjunto de cinco mangos de marfil época ibérica (s. VI – s. I a. C.). Son objetos con características técnicas, formales y decorativas muy similares entre sí, lo que que permite plantear una relación entre ellos en su proceso de producción. Sin embargo, fueron recuperados en cuatro yacimientos diferentes del área ibérica: los poblados de Turó de Montgròs (El Brull, Barcelona) y La Serreta (Alcoi, Alicante) y las necrópolis de El Cigarralejo (Mula, Murcia) y Coimbra del Barranco Ancho (Jumilla, Murcia), en esta última, se recuperaron dos de ellos. Todas las piezas, por sus contextos arqueológicos se datan entre el s. IV y principios del s. II a. C. Los análisis se llevaron a cabo con el objetivo de identificar la naturaleza y procedencia de las incrustaciones de carácter decorativo y la sustancia adherente todavía presentes en estos mangos. Si bien, en algunos de ellos, debido a su deteriorado estado de conservación, únicamente quedaban las improntas de las incrustaciones y no había restos aparentes de la sustancia de tono gris-negro que, presumiblemente, serviría para adherir las incrustaciones. Las piezas mejor conservadas son las recuperadas en lugares de hábitat. Los estudios se han realizado mediante técnicas no destructivas que no comprometiesen la integridad de las piezas. Así, se llevaron a cabo análisis por Fluorescencia de Rayos X (XRF), y por Espectrofotometría de Infrarrojo Cercano por Transformada de Fourier (FT-NIR). Todo ello se complementó mediante la revisión de los mangos con un microscopio electrónico de barrido equipado con un Sistema de Rayos X de Energía Dispersiva (SEM-EDAX-Sapphire), un microscopio óptico SMZ (NIKON) y un microscopio digital Dino-lite mod. AM7115MZT EDGE de 10x a 200x con una luz incidente por medio de un iluminador de fibra óptica y dotado de un software con funciones de medición integrales, para obtener imágenes de alta precisión. El análisis de XRF ha permitido identificar como estaño la sustancia empleada para adherir las incrustaciones decorativas en la pieza, empleando una técnica de tipo soldadura blanda. El FTNIR, por su parte, ha revelado que dichas incrustaciones fueron realizadas sobre resinas fósiles, muy probablemente ámbar. Estos resultados resultan totalmente novedosos dentro del mundo artesanal de época ibérica y, por tanto, de gran interés, evidenciando el valor de estas piezas en las que materias primas de presencia escasa en el mundo ibérico como son el marfil y el ámbar aparecen combinadas; así como el uso del estaño a modo de soldadura blanda nos revela procesos de manufactura no atestiguados hasta el momento en las industrias sobre materias duras de origen animal de la Edad del Hierro en la Península Ibérica. Cabe destacar que la realización de análisis químicos sobre piezas arqueológicas aporta datos específicos, prácticamente imposibles de obtener en un estudio macro o microscópico de los artefactos. Por ello, desde el proyecto proyecto “Madera, hueso, marfil, asta, concha ¿Artesanías marginales o marginadas?” (HAR2013-45770-P y ACOMP/2015/256) (financiado por el Ministerio de Economía y Competitividad y la Generalitat Valenciana) dirigido por la Dra. Consuelo Mata, se ha apostado por desarrollar estudios interdisciplinares, que impliquen el contacto y la comunicación entre distintos especialistas con la finalidad de conseguir resultados más sólidos y transversales

EcoCyc: fusing model organism databases with systems biology.

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc

The impact of genetic selection on greenhouse-gas emissions in Australian dairy cattle

In Australia, dairy cattle account for ~12% of the nation’s agricultural greenhouse-gas (GHG) emissions. Genetic selection has had a positive impact, reducing GHG emissions from dairy systems mainly due to increased production per cow, which has led to (1) requiring fewer cows to produce the same amount of milk and (2) lowering emissions per unit of milk produced (emission intensity). The objective of the present study was to evaluate the consequences of previous and current genetic-selection practices on carbon emissions, using realised and predicted responses to selection for key traits that are included in the Australian national breeding objective. A farm model was used to predict the carbon dioxide equivalent (CO₂-eq) emissions per unit change of these traits, while holding all other traits constant. Estimates of the realised change in annual CO₂-eq emissions per cow over the past decade were made by multiplying predicted CO₂-eq emissions per unit change of each trait under selection by the realised rates of genetic gain in each of those traits. The total impact is estimated to be an increase of 55 kg CO₂-eq/cow.year after 10 years of selection. The same approach was applied to future CO₂-eq emissions, except predicted rates of genetic gain assumed to occur over the next decade through selection on the Balanced Performance Index (BPI) were used. For an increase of AU$100 in BPI (~10 years of genetic improvement), we predict that the increase of per cow emissions will be reduced to 37 kg CO₂-eq/cow.year. Since milk-production traits are a large part of the breeding goal, the GHG emitted per unit of milk produced will reduce as a result of improvements in efficiency and dilution of emissions per litre of milk produced at a rate estimated to be 35.7 g CO₂-eq/kg milk solids per year in the past decade and is predicted to reduce to 29.5 g CO₂-eq/kg milk solids per year after a conservative 10-year improvement in BPI (AU$100). In fact, cow numbers have decreased over the past decade and production has increased; altogether, we estimate that the net impact has been a reduction of CO₂-eq emissions of ~1.0% in total emissions from the dairy industry per year. Using two future scenarios of either keeping the number of cows or amount of product static, we predict that net GHG emissions will reduce by ~0.6%/year of total dairy emissions if milk production remains static, compared with 0.3%/year, if cow numbers remain the same and there is genetic improvement in milk-production traits

Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis

The preterm gut microbiome is a complex dynamic community influenced by genetic and environmental factors and is implicated in the pathogenesis of necrotising enterocolitis (NEC) and sepsis. We aimed to explore the longitudinal development of the gut microbiome in preterm twins to determine how shared environmental and genetic factors may influence temporal changes and compared this to the expressed breast milk (EBM) microbiome. Stool samples (n = 173) from 27 infants (12 twin pairs and 1 triplet set) and EBM (n = 18) from 4 mothers were collected longitudinally. All samples underwent PCR-DGGE (denaturing gradient gel electrophoresis) analysis and a selected subset underwent 454 pyrosequencing. Stool and EBM shared a core microbiome dominated by Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae. The gut microbiome showed greater similarity between siblings compared to unrelated individuals. Pyrosequencing revealed a reduction in diversity and increasing dominance of Escherichia sp. preceding NEC that was not observed in the healthy twin. Antibiotic treatment had a substantial effect on the gut microbiome, reducing Escherichia sp. and increasing other Enterobacteriaceae. This study demonstrates related preterm twins share similar gut microbiome development, even within the complex environment of neonatal intensive care. This is likely a result of shared genetic and immunomodulatory factors as well as exposure to the same maternal microbiome during birth, skin contact and exposure to EBM. Environmental factors including antibiotic exposure and feeding are additional significant determinants of community structure, regardless of host genetics

Characterization of glandular trichomes of Minthostachys verticillata “peperina” from northwest and central Argentina: relation with essential oil content

Minthostachys verticillata is an endemic species in Argentina that shows higher contents of essential oils (EO %, v/w) in plants from the central area than in those from the northwest. Although the reason for this difference is still unknown, studies on species from this family indicate that the variation in essential oil yields could be due to genetic or environmental factors or their interaction, which modifies the number and size of the glandular trichomes, structures where the oil is synthesized and stored. The main objective of this study was to analyze the density and size of glandular trichomes on M. verticillata leaves and their relation to the EO in wild plants from northwestern (NA) and central Argentina (CA); and then in a semi controlled environment, we studied the relation between the density and size of these to the leaf size (apical vs basal leaves) and plant origin. For the first experiment, we collected random wild plants in the main natural areas of distribution; and in the second one, we used cloned plants and grew them in a completely randomized design. The analyses of the trichome density and size and the EO% were carried out using a transmission electron microscope and a Clevenger type trap respectively. The wild plants from the central area showed larger glandular trichomes and higher EO concentrations; in addition, under semi-controlled conditions, we also found a greater number of trichomes per mm2 in both apical and basal leaves in the plant from CA than in that from NA. Thus, the trichome size and number were affected in a different way by the environment.Instituto de Recursos BiológicosFil: Arteaga, Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Collado, Cristian Emanuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Gil, Alejandra. Universidad de Buenos Aires. Facultad de Agronomía; Argentin

Optimal designs for a non-linear model for the pharmacokinetics of ethanol elimination in the human body

This research was partially supported by the Spanish Ministry of Science, Innovation and Universities project PID2021-125211OB-I00 (all authors), the Spanish Junta de Castilla y León project ‘SA105P20’ (J.M. R-D and M.T. S-M) and by the Spanish MINECO project PGC2018- 098623-B-I00 (I. M-C)

Factors influencing gastrointestinal tract and microbiota immune interaction in preterm infants

The role of microbial colonization is indispensable for keeping a balanced immune response in life. However, the events that regulate the establishment of the microbiota, their timing, and the way in which they interact with the host are not yet fully understood. Factors such as gestational age, mode of delivery, environment, hygienic measures, and diet influence the establishment of microbiota in the perinatal period. Environmental microbes constitute the most important group of exogenous stimuli in this critical time frame. However, the settlement of a stable gut microbiota in preterm infants is delayed compared to term infants. Preterm infants have an immature gastrointestinal tract and immune system which predisposes to infectious morbidity. Neonatal microbial dynamics and alterations in early gut microbiota may precede and/or predispose to diseases such as necrotizing enterocolitis (NEC), late-onset sepsis or others. During this critical period, nutrition is the principal contributor for immunological and metabolic development, and microbiological programming. Breast milk is a known source of molecules that act synergistically to protect the gut barrier and enhance the maturation of the gut-related immune response. Host-microbe interactions in preterm infants and the protective role of diet focused on breast milk impact are beginning to be unveiled.M.C. acknowledges a “Rio Hortega” Research Fellowship Grant (CM13/0017) and M.V. acknowledges grants PI11/0313 and RD12/0026/0012 (Red SAMID) from the Instituto Carlos III (Spanish Ministry of Economy and Competitivity). M.C.C. and G.P-M. were supported by the grant AGL2013-47420-R from the Spanish Ministry of Science and Innovation.Peer reviewe