Search

Climate change is modifying the spatiotemporal patterns of global precipitation events, temperatures, and winds, therefore, after extreme events, improving emergency responses in urban areas is key to saving its inhabitants. In Southern America, the number of extreme events is increasing. This is the case of Soledad, the municipality in Colombia where most of the catastrophic wind phenomena take place. To date, no studies have been conducted to quantify the impacts and effects of the urban cyclonic wind phenomena on society and the urban built environment. This lack of information and dissemination means that the population is not informed of the magnitude of the problem. This research aims to generate a risk map of atmospheric wind phenomena to evaluate their impacts and establish spatial-temporal correlations based on meteorological data from the last 20 years. Moreover, the online press has been used to identify the location of these phenomena and their negative impacts over time. For each event, the following indicators have been studied: (1) location of the atmospheric wind events; (2) occurrence rate; (3) impact of the events discriminated by fatalities, injuries, and affected houses. The results show that in 20 years, a total of 34 urban cyclonic wind events were reported. Those occurrences have impacted 60 neighbourhoods, leaving 7 deaths, 14,552 injured, and 5180 affected homes. These findings show the magnitude of the problem and the need to inform the population to improve emergency responses. We conclude that effective consideration of the resulting map will be crucial in the processes of decision-making related to territorial planning in Soledad, but also in other Southern American cities., Universidad de Granada / CBUA

Summary Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium’s annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome, and 16 regulators that indirectly affect transcription. Only 20% of transcriptional regulation is mediated by canonical TFs when responding to perturbations. Using a Random Forest, we quantified the non-redundant contribution of different mechanisms such as supercoiling, metabolic control, RNA degradation, and chromosome topology to transcriptional changes. Model-predicted gene changes correlate well with experimental data in 95% of the tested perturbations, explaining up to 70% of the total variance when also considering noise. This analysis highlights the importance of considering non-TF-mediated regulation when engineering bacteria., Graphical Abstract, Highlights • Full comprehensive reconstruction of a bacterial gene regulatory network achieved • Genome-reduced bacterium Mycoplasma pneumoniae is robust to genetic perturbations • Large part of transcription regulation in bacteria is transcription-factor independent • Transcription-factor-independent regulation has a smaller dynamic range, We have achieved a comprehensive reconstruction of a gene regulatory network in a genome-reduced bacterium, Mycoplasma pneumoniae. With this network, we observed that a large part of transcription regulation is determined by non-canonical factors such as DNA supercoiling, riboswitches, and genome organization or RNA-mediated regulation. This analysis highlights the importance of considering non-transcription-factor (TF)-mediated regulation when engineering bacteria.

In this chapter the capsaicin derivative grafting onto cellulose ispresented as an alternative to obtain bioactive papers. First, grafting of nonivamide (capsaicin derivative) onto cellulose fibers using polycarboxylicacid as linking agent is discussed. The effect of different reaction variables(namely, time, temperature, and catalyst amount), on reaction occurrenceand efficacy is analyzed. From this data, the optimal reaction conditionsare selected and then grafting reaction is applied to commercial paper sheets. Final properties like antioxidant, insect repellent, and antimicrobialactivity, as well as mechanical properties of the modified paper are presentedand discussed. Fil: Muratore, Florencia. Universidad Nacional de Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada; Argentina Fil: Goñi, Maria Laura. Universidad Nacional de Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada; Argentina Fil: Serrano, Luis. Universidad de Córdoba; España Fil: Labidi, Jalel. Universidad del País Vasco; España Fil: Barbosa, Silvia Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina Fil: Martini, Raquel Evangelina. Universidad Nacional de Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada; Argentina

The understanding of interaction dynamics in signaling pathways can shed light on pathway architecture and provide insights into targets for intervention. Here, we explored the relevance of kinetic rate constants of a key upstream osmosensor in the yeast high-osmolarity glycerol-mitogen-activated protein kinase (HOG-MAPK) pathway to signaling output responses. We created mutant pairs of the Sln1-Ypd1 complex interface that caused major compensating changes in the association (kon) and dissociation (koff) rate constants (kinetic perturbations) but only moderate changes in the overall complex affinity (Kd). Yeast cells carrying a Sln1-Ypd1 mutant pair with moderate increases in kon and koff displayed a lower threshold of HOG pathway activation than wild-type cells. Mutants with higher kon and koff rates gave rise to higher basal signaling and gene expression but impaired osmoadaptation. Thus, the kon and koff rates of the components in the Sln1 osmosensor determine proper signaling dynamics and osmoadaptation. The work was supported by European Commission 7th Framework Programme (UNICELLSYS, grant 201142 to L.S., F.P., and E.K.), grants from the Spanish Ministry of Economy and Competitiveness (BFU2012-33503 and FEDER, BFU2014-52125-REDT, BFU14-51672-REDC, and BFU2015-64437-P to F.P.; BFU2014-52333-P to E.d.N.), the Catalan Government (2014 SGR 599), an ERC Advanced Grant 294294 from the EU 7th Framework Programme (SYNCOM, to F.P.), the Fundación Botín, Banco Santander (through its Santander Universities Global Division, to F.P.), and the German Research Council (RTG 1772Computational Systems Biology to E.K.). F.P. and E.d.N. are recipients of an ICREA Acadèmia (Generalitat de Catalunya). This work was supported by the Spanish Ministerio de Economía y Competitividad, Plan Nacional, and the European Fund for Regional Development (BIO2012-39754 to L.S.). We acknowledge support of the Spanish Ministry of Economy and Competitiveness, “Centro de Excelencia Severo Ochoa 2013-2017” (SEV-2012-0208). We acknowledge the support of the CERCA Programme/Generalitat de Catalunya.

Transcription is a core process of bacterial physiology, and as such it must be tightly controlled, so that bacterial cells maintain steady levels of each RNA molecule in homeostasis and modify them in response to perturbations. The major regulators of transcription in bacteria (and in eukaryotes) are transcription factors. However, in genome-reduced bacteria, the limited number of these proteins is insufficient to explain the variety of responses shown upon changes in their environment. Thus, alternative regulators may play a central role in orchestrating RNA levels in these microorganisms. These alternative mechanisms rely on intrinsic features within DNA and RNA molecules, suggesting they are ancestral mechanisms shared among bacteria that could have an increased relevance on transcriptional regulation in minimal cells. In this review, we summarize the alternative elements that can regulate transcript abundance in genome-reduced bacteria and how they contribute to the RNA homeostasis at different levels. We acknowledge support of the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program under agreement No 670216 (MYCOCHASSIS) and the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013-2017′.

Summary Coordination of transcription in bacteria occurs at supra-operonic scales, but the extent, specificity, and mechanisms of such regulation are poorly understood. Here, we tackle this problem by profiling the transcriptome of the model organism Mycoplasma pneumoniae across 115 growth conditions. We identify three qualitatively different levels of co-expression corresponding to distinct relative orientations and intergenic properties of adjacent genes. We reveal that the degree of co-expression between co-directional adjacent operons, and more generally between genes, is tightly related to their capacity to be transcribed en bloc into the same mRNA. We further show that this genome-wide pervasive transcription of adjacent genes and operons is specifically repressed by DNA regions preferentially bound by RNA polymerases, by intrinsic terminators, and by large intergenic distances. Taken together, our findings suggest that the basal coordination of transcription is mediated by the physical entities and mechanical properties of the transcription process itself, and that operon-like behaviors may strongly vary from condition to condition., Graphical Abstract, Highlights • Basal coordination of transcription is driven by pervasive transcription • It is repressed by terminators, long intergenic regions, and stalled RNA polymerases • Operon-like behaviors may strongly vary from condition to condition, By analyzing multiple transcriptomes and structural features of a minimal bacterial genome, Junier et al. show that the basal coordination of transcription in bacteria relies on the capacity of RNA polymerases to transcribe consecutive genes and operons in one go. Stalled RNA polymerases, large intergenic regions, and intrinsic terminators delineate genomic domains of this coordination, for which operon-like behaviors may strongly vary from condition to condition.

This chapter is devoted to the fabrication and advanced characterization of cobalt nanowires grown by focused electron beam induced deposition. After showing how to pattern pure Cobalt wires by choosing appropriate growth conditions, we investigate the conduction of domain walls in this type of nanowires for storage and logic applications. Moreover, we pattern out-of-plane nanostructures, opening a new route to investigate three-dimensional spintronic systems.

In this paper, an optimization process, based on a genetic algorithm, is presented for the minimization of the cost (including losses) of ferromagnetic and conductive shields. The purpose of these shields is to maintain the power frequency magnetic field generated by underground power cable duct banks below a certain threshold, without limiting the ampacity of the mitigated cable. Both horizontal and reverse-U shielding geometries are tested through their application to a case study composed of 9 (3 × 3) ducts where two balanced in-phase three-phase circuits are arranged in three configurations: vertical, horizontal and triangular. The area to be shielded is located above ground surface at one side of the trench axis, where dwellings are usually present. The associated electromagnetic-thermal problem is solved in the optimization process by means of the finite element method. The most suitable solutions are identified, by highlighting the key features of each shield (material and geometry). Further scenarios, such as the addition of a third three-phase circuit in the shielded duct bank, are also analyzed., This work was supported by the regional Government of Guandong Province under grant P09-TEP-5170.

This chapter brings mammalian signal transduction to the center of quantitative and integrative sciences. Historically imbedded within human physiology, thanks to proteomics, interactomics, and molecular biology approaches, signaling is now far beyond the “black box” principle. However, despite the large amount of data available, we still have only limited insight into general design principles, and we lack knowledge on how cell type-specific signaling is achieved. Here, we summarize recent efforts in elucidating cell type-specific signaling, and in particular the role of protein abundances, signaling complexes and modules. We further discuss the potential of using synthetic biology approaches to decipher signaling networks. All of this is discussed in light of complementary quantitative mathematical modeling approaches. Signaling, more than any other discipline, needs computational biology to capture the dynamic systems behavior, and to reach its final goal: to be truly predictive for both the physiological and disease perturbed cellular conditions.

A generalized procedure for the in situ application of magnetic fields by means of the excitation of the objective lens for magnetic imaging experiments in Lorentz microscopy and electron holography is quantitatively described. A protocol for applying magnetic fields with arbitrary in-plane magnitude and orientation is presented, and a freeware script for Digital Micrograph¿ is provided to assist the operation of the microscope. Moreover, a method to accurately reconstruct hysteresis loops is detailed. We show that the out-of-plane component of the magnetic field cannot be always neglected when performing quantitative measurements of the local magnetization. Several examples are shown to demonstrate the accuracy and functionality of the methods., This work was supported by the Spanish Ministry of Economy and Innovation (MINECO) through Projects MAT2009-08771, MAT2011-28532-C03-02, MAT2011-28532-C03-03 and MAT2011-27553-C02 including FEDER funding, by the Aragón Regional Government through Projects E26 and CTPP4/11, and the European Union under the Seventh Framework Programme under a contract for an Integrated Infrastructure Initiative, Reference 312483-ESTEEM2.

Human skin copes with harmful environmental factors that are circadian in nature, yet how circadian rhythms modulate the function of human epidermal stem cells is mostly unknown. Here we show that in human epidermal stem cells and their differentiated counterparts, core clock genes peak in a successive and phased manner, establishing distinct temporal intervals during the 24 hr day period. Each of these successive clock waves is associated with a peak in the expression of subsets of transcripts that temporally segregate the predisposition of epidermal stem cells to respond to cues that regulate their proliferation or differentiation, such as TGFβ and calcium. Accordingly, circadian arrhythmia profoundly affects stem cell function in culture and in vivo. We hypothesize that this intricate mechanism ensures homeostasis by providing epidermal stem cells with environmentally relevant temporal functional cues during the course of the day and that its perturbation may contribute to aging and carcinogenesis. This work has been funded by an ERC Consolidator Grant (STEMCLOCK) to S.A.B. and by the PROSPECTS, grant agreement number HEALTH-F4-2008-201648, to L.S. from the European Union. G.S. is funded by an AXA Fund fellowship. K.T. is funded by a La Caixa Ph.D. fellowship./nResearch in the lab of B.L. is funded by the European Research Council (ERC), MINECO Plan Nacional grant BFU2011-26206, ERASysBio+ ERANET project EUI2009-04059 GRAPPLE, the EMBO Young Investigator Program, EU Framework 7 project 277899 4DCellFate, and the EMBL/CRG Systems Biology Program

In recent years, high-throughput discovery of macromolecular protein structures and complexes has played a major role in advancing a more systems-oriented view of protein interaction and signaling networks. The design of biological systems often employs structural information or structure-based protein design to successfully implement synthetic signaling circuits or for rewiring signaling flows. Here, we summarize the latest advances in using structural information for studying protein interaction and signaling networks, and in synthetic biology approaches. We then provide a perspective of how combining structural biology with engineered cell signaling modules--using additional information from quantitative biochemistry and proteomics, gene evolution, and mathematical modeling--can provide insight into signaling modules and the general design principles of cell signaling. Ultimately, this will improve our understanding of cell- and tissue-type-specific signal transduction. Integrating the quantitative effects of disease mutations into these systems may provide a basis for elucidating the molecular mechanisms of diseases. The work was supported by the EU (PROSPECTS, grant agreement number 201648, and PRIMES, grant agreement number 278568)

Chemically unmodified sodium hyaluronate has been crosslinked by photoinduced decomposition of a trifunctional diazonium salt to generate new biomaterials. In addition, the photocrosslinking process does not require a photoinitiator. Thin films of formulations of sodium hyaluronate and the photocrosslinker at different percentages have been processed. Cytotoxicity has been explored and toxicity was not observed with the selected cell lines. 2D patterns of controlled geometry have been generated by direct laser writing to perform cell adhesion studies. Different adhesion behavior of the cell lines, as assessed by vinculin immunostaining and scanning electron microscopy, has been observed in the polymeric films depending on the degree of photocrosslinking. © 2012 Elsevier Ltd., This work was supported by the Spanish MEC project MAT2011-27978-C02 and MAT2011-26851-C02-01, ARAID project for young scientists, ERC-Starting Grant NANOPUZZLE and FEDER funding (EU). M. Lomba thanks the Gobierno de Aragón (Spain) for a PhD. Grant. JM de la Fuente thanks ARAID for financial support. B. Saez Gutiérrez thanks ISCIII for financial support (Sara Borrell CD09/00174).

With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. In this chapter, we present a simple and powerful method to either know the DNA specificity of a wild-type protein or design new specificities by using the protein design algorithm FoldX. The only basic requirement is having a good resolution structure of the complex. Protein-DNA interaction design may aid the development of new parts designed to be orthogonal, decoupled, and precise in its target. Further, it could help to fine-tune the systems in terms of specificity, discrimination, and binding constants. In the age of newly developed devices and invented systems, computer-aided engineering promises to be an invaluable tool.

4 pages, 3 figures., Composites were synthesized by “in-situ” polymerization of polyazomethine, a liquid crystal polymer (LCP), in presence of multi-walled carbon nanotubes (MWNTs) previously dispersed in one of the employed monomers. Fiber processing was carried out by extrusion from the composites containing 1 and 10 wt.% of MWNTs at the mesophase temperature. We have observed that the typical highly oriented internal fibrillar structure can be significantly disrupted by increasing the nanotube content in the composite fibers. Evidences of MWNT alignment were found in the studied LCP/MWNT composites., Funded by the Gobierno de Aragón (Spain). E.M. acknowledges support from MEC (Ramón y Cajal Program).

8 pages, 7 figures, 3 tables., New poly(methacrylate) copolymers containing 90 mol% of a promesogenic unit based on the 4-butoxybenzanilide, 4-cyanobiphenyl or 4-cyanoterphenyl cores and 10 mol% of a photosensitive push–pull substituted 4-(N-methylamino)-4′-nitrostilbene group have been prepared. All polymers are liquid crystalline and thermally stable with decomposition temperatures above 320 °C. The irradiation with linearly polarised light (either 325, 365 or 488 nm) results in the induction of a small optical anisotropy in the films due to an angular-selective photoreaction, whereas the absorbance perpendicular to the electric field vector of the incident light becomes larger compared to the absorbance parallel to it. In films of the copolymer containing 4-cyanobiphenyl and 4-(N-methylamino)-4′-nitrostilbene units, the anisotropy was significantly enhanced by annealing above Tg up to a dichroism D = 0.5. A thin film aligned by this procedure shows an anisotropic red emission with a ratio of 2.8 between emission intensities in the parallel and perpendicular directions due to the presence of oriented fluorescent stilbene units., This work was supported by the EC Brite/Euram project BE97-4210 Photoflu, the CICYT–FEDER Spanish projects MAT 2002-04118-C02-01 and MAT 2003-07806-C02-01, the Government of Aragon and the Programas Ramón y Cajal and FPI (MCyT–MEC, Spain).

This chapter focuses mainly on the performance of ab initio methods for the description of spectroscopic molecular properties of compounds. Most of the quantum-chemical methods developed up to date are based on the concept of the one-electron wave function. The electronic states of a system with N electrons are described by a double expansion. Molecular orbitals (MOs) are one-electron wave functions expressed as linear combinations of a known one-electron basis set (K) and the N electron wave function is formulated in a many-electron basis set formed by determinants (or linear combination of them to form spin-adapted wave functions), built as normalized antisymmetric products of MOs. According to the number of configurations considered, the methods are classified in the following two categories: (1) Single-configuration methods—they are typically based in the Hartree-Fock (HF) reference, which determines the MOs. The electron correlation treatment is usually performed at the configuration interaction (CI), coupled-cluster (CC) or Moller-Plesset (MP) levels. (2) Multiconfigurational methods—part of the electronic correlation is already included in the reference wave function, normally by using a MCSCF wave function that determines a set of MOs. The remaining electron correlation effects are accounted for by muti-reference CI (MRCI), multireference coupled-cluster (MRCC) or multireference perturbation theory (MRPT) techniques.

Publisher Summary This chapter describes the relationship between sequence and structure in α-helices, β-hairpins, and β- sheets. First, there is an analysis regarding the individual conformational preferences of 20 amino acids. These tendencies could explain the conformational preferences detected in the random coil state, as well as the secondary structure propensities of the 20 amino acids. This is followed by a description of the extent of the knowledge regarding α-helices. The α-helix is the best known and most easily recognized of the polypeptide regular structures. The chapter focuses on β-hairpins and β-sheets, about which much less is known. Finally, the importance of secondary structure elements in protein folding and stability is discussed. Kinetic analysis of proteins with stabilized α-helices demonstrates that an increase in the contribution of favorable local native interactions can, in some cases, optimize folding rates. Essentially, when a secondary structure element is folded in the transition state, its stabilization will accelerate folding. As in the case of the protein stabilization the increase in folding speed will not be equivalent to the stabilization of the secondary structure element, since the denatured state will also be stabilized.

This review serve to open the field to many coordination chemistry who can use specific expertise of new transition metal liquid crystals. Bibliography

The complexes [RhCl(COD)L] (COD = cyclocta-1,5-diene; L = NC5H4CH=NC6H4OCnH2n+1) have been prepared by reaction of the corresponding L (n = 8, 14) ligands with [RhCl(COD)]2. They react with CO to give cis-[RhCl(CO)2L] (n = 2, 4, 6–10, 12, 14). Reaction of cis-dicarbonyl compounds with L in the presence of Me3NO gives trans-[RhCl(CO)L2] (n = 4, 8). Monocarbonyl compounds of formulae [RhCl(CO)L(P(OMe)3)] (n = 6, 8, 14) have been made by reaction of cis-[RhCl(CO)2L] with P(OMe)3 in dichloromethane. The mesogenic properties of the compounds [RhCl(CO)2L] (n = 8–10, 12, 14) are described.

1. Trypsin preferentially cleaves the α subunit of depolymerized tubulin or vinblastine induced aggregates (in which longitudinal interactions between tubulin molecules could take place). 2. No cleavage was found for tubulin polymerized into microtubules (containing lateral and longitudinal tubulin interactions), in the presence of taxol. 3. In the presence of colchicine or podophyllotoxin the α subunit was partially protected from proteolytic digestion. 4. Trypsin digestion pattern varied upon the addition of different concentrations of griseofulvin. At the higher concentration used, in which microtubules assembly was inhibited, both tubulin subunits were cleaved., This work was supported in part by grants from Comision Asesora de Investigacion Cientifica y Tecnica and Fondo de Investigaciones Sanitarias.

Calcium has been suggested to be an important element in the regulation of microtubule dynamics ‘in vivo’. In this report we have analyzed the possibility that microtubule-associated protein 2 (MAP2) binds calcium. MAP2 was blue-stained with the cationic carbocyanine dye ‘stains-all’ in a similar way to that of calcium-binding proteins and bound 45Ca as estimated from dot-blotting experiments. The calcium-blotting characateristics of MAP2, determined by equilibrium dialysis, indicated that MAP2 bound about 3 mol (n = 2.69 ± 0.4)_of calcium per mol of proein (Kd = (0.9 ± 0.2) · 10−5 M). Analysis of the Scatchard plots from equilibrium dialysis and dot-blot assays indicated that MAP2 also presented low-affinity calcium-binding sites (Kd = (0.3 ± 0.2) · 10−4 M). Incubation of nitrocellulose blots of proteolytically digested MAP2 with 45Ca indicated that the calcium-binding sites were located in the region that is not involved in the interaction with tubulin (projection region).

Vinblastine induces brain tubulin to assemble into spirals. This process is stimulated by microtubule-associated proteins (MAPs) which copolymerize with brain microtubules assembled in vitro. When the carboxy terminal of tubulin is removed by subtilisin digestion, vinblastine readily induces the aggregation of tubulin into spiral-like or circular structures, even in the absence of MAPs. These results suggest that in the absence of MAPs, the carboxy-terminal domain of tubulin may inhibit vinblastine-induced polymerization of tubulin into spiral-like structures.