Phosphorylation at the N-terminal finger subdomain of a viral RNA-dependent RNA polymerase

The RNA-dependent RNA polymerase (RdRP) of the Hepatitis C virus (HCV), named NS5B, is phosphorylated by the cellular protein kinase C-related kinase 2 (PRK2) at two serine residues (Ser29 and Ser42) of the finger subdomain (genotype 1b). Herein, using bioinformatics, we selected four potential phosphorylation residues (Ser46, Ser76, Ser96 and Ser112) of NS5B (genotype 2a) for study. Whereas the NS5B Ser46D and Ser76D substitutions seemed to improve polymerase activity, the Ser96D mutation decreased colony formation efficiency. Active WT NS5B was utilized in in vitro kinase assays, and phosphopeptides were analyzed by mass spectrometry. Interestingly, the data indicated that both the NS5B Ser29 and Ser76 residues resulted phosphorylated. Thus, as Ser76 is absolutely conserved across HCV genotypes, our results confirmed the relevance of these sites for both genotypes and suggested that Ser76 becomes phosphorylated by a cellular kinase different from PRK2. By molecular dynamic simulations, we show that new interactions between space-adjacent amino acid chains could be established by the presence of a di-anionic phosphate group on the analyzed serines to possibly modify RNA polymerase activity. Together, our data present novel evidence on the complex regulation at the finger subdomain of HCV NS5B via phosphorylation.

Bioinformatics and Moonlighting Proteins

Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyze and describe several approaches that use sequences, structures, interactomics, and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are (a) remote homology searches using Psi-Blast, (b) detection of functional motifs and domains, (c) analysis of data from protein–protein interaction databases (PPIs), (d) match the query protein sequence to 3D databases (i.e., algorithms as PISITE), and (e) mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs) has the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations – it requires the existence of multialigned family protein sequences – but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/), previously published by our group, has been used as a benchmark for the all of the analyses.

Structural parameters effect on the electrical and electroluminescence properties of silicon nanocrystals/SiO2 superlattices

The effect of the oxide barrier thickness (tSiO2) reduction and the Si excess ([Si]exc) increase on the electrical and electroluminescence (EL) properties of Si-rich oxynitride (SRON)/SiO2 superlattices (SLs) is investigated. The active layers of the metal-oxide-semiconductor devices were fabricated by alternated deposition of SRON and SiO2 layers on top of a Si substrate. The precipitation of the Si excess and thus formation of Si nanocrystals (NCs) within the SRON layers was achieved after an annealing treatment at 1150 °C. A structural characterization revealed a high crystalline quality of the SLs for all devices, and the evaluated NC crystalline size is in agreement with a good deposition and annealing control. We found a dramatic conductivity enhancement when the Si content is increased or the SiO2 barrier thickness is decreased, due to a larger interaction of the carrier wavefunctions from adjacent layers. EL recombination dynamics were studied, revealing radiative recombination decay times of the order of tens of microseconds. Lower lifetimes were found at higher [Si]exc, attributed to exciton confinement delocalization, whereas intermediate barrier thicknesses present the slowest decay. The electrical-to-light conversion efficiency increases monotonously at thicker barriers and smaller Si contents. We ascribe these effects mainly to free carriers, which enhance carrier transport through the SLs while strongly quenching light emission. Finally, the combination of the different results led us to conclude that tSiO2 ∼ 2 nm and [Si]exc from 12 to 15 at% are the ideal structure parameters for a balanced electro-optical response of Si NC-based SLs.

Observation of Room Temperature Photoluminescence from Asymmetric CuGaO2/ZnO/ZnMgO Multiple Quantum Well Structures

Asymmetric (CuGaO2/ZnO/ZnMgO) and symmetric (ZnMgO/ZnO/ZnMgO) multiple quantum well (MQW) structures were successfully fabricated using pulsed laser deposition (PLD) and their comparison were made. Efficient room temperature photoluminescent (PL) emission was observed from these MQWs and temperature dependent luminescence of asymmetric and symmetric MQWs can be explained using the existing theories. A systematic blue shift was observed in both MQWs with decrease in the confinement layer thickness which could be attributed to the quantum confinement effects. The PL emission from asymmetric and symmetric MQW structures were blue shifted compared to 150 nm thick ZnO thin film grown by PLD due to quantum confinement effects.

Green and low-cost synthesis of PANI–TiO2 nanocomposite mesoporous films for photoelectrochemical water splitting

Green and low-cost synthesis procedure for preparation of PANI/TiO₂ mesoporous nanocomposite films with enhanced photocatalytic performance, thanks to a synergic reaction mechanism between PANI and TiO₂ under UV light irradiation.

Evidence for multiple paternity in the school shark Galeorhinus galeus found in New Zealand waters

This study assessed the levels of relatedness of Galeorhinus galeus of progeny arrays using six microsatellite DNA markers. A parentage analysis from five families (mother and litter) from the North Island of New Zealand suggested the occurrence of genetic polyandry in G. galeus with two of the five litters showing multiple sires involved in the progeny arrays. This finding may be consistent with the reproductive characteristics of G. galeus, in which females can potentially store sperm for long periods of time after the mating season.

Detection of residual organochlorine and organophosphorus pesticides in agricultural soil in Rio Verde region of San Luis Potosi, Mexico

Organochlorine pesticides were intensively used in Mexico from 1950 until their ban and restriction in 1991. However, the presence of these compounds is commonly reported in many regions of the country. The aim of the present study was to identify and quantify residual organochlorine and organophosphorus pesticides in agricultural soil in Rio Verde region, San Luis Potosi state, which has been identified as possibly polluted by pesticides. Composed samples from 24 zones covering an area of approximately 5,440 ha were analyzed. The most frequently found pesticides were p,p'-DDT followed by ,p,p'-DDE, heptachlor, endosulfan and γ-HCH whose frequency rates were 100, 91, 83 and 54%, respectively. The concentration of p,p'-DDT in the crops grown in these soils was in the following order: chili > maize > tomato > alfalfa. The results obtained in this study show that p,p'-DDT values are lower or similar to those found in other agricultural regions of Mexico. Methyl and ethyl parathion were the most frequent organophosphate pesticide detected in 100% and 62.5% of the samples with average concentrations of 25.20 and 47.48 μg kg(-1), respectively. More research is needed to establish the background levels of pesticides in agricultural soils and their potential ecological and human health effects in this region.

MultitaskProtDB: a database of multitasking proteins

We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth.

A comparative study of fungal and bacterial biofiltration treating a VOC mixture

Bacterial biofilters usually exhibit a high microbial diversity and robustness, while fungal biofilters have been claimed to better withstand low moisture contents and pH values, and to be more efficient coping with hydrophobic volatile organic compounds (VOCs). However, there are only few systematic evaluations of both biofiltration technologies. The present study compared fungal and bacterial biofiltration for the treatment of a VOC mixture (propanal, methyl isobutyl ketone-MIBK, toluene and hexanol) under the same operating conditions. Overall, fungal biofiltration supported lower elimination capacities than its bacterial counterpart (27.7 ± 8.9 vs 40.2 ± 5.4 gCm(-3) reactor h(-1)), which exhibited a final pressure drop 60% higher than that of the bacterial biofilter due to mycelial growth. The VOC mineralization ratio was also higher in the bacterial bed (≈ 63% vs ≈ 43%). However, the substrate biodegradation preference order was similar for both biofilters (propanal>hexanol>MIBK>toluene) with propanal partially inhibiting the consumption of the rest of the VOCs. Both systems supported an excellent robustness versus 24h VOC starvation episodes. The implementation of a fungal/bacterial coupled system did not significantly improve the VOC removal performance compared to the individual biofilter performances.

Evaluating Internet information on attention-deficit/hyperactivity disorder (ADHD) treatment: parent and expert perspectives

BACKGROUND

The Internet is increasingly used as a source of health-related information. The objective of this study was to assess the quality of web-based information on treatments for attention-deficit/hyperactivity disorder (ADHD).

METHODS

Sixteen expert health professionals in ADHD and 35 parents of paediatric patients with a recent diagnosis of ADHD assessed the information contained in the 10 highest ranked websites in Spanish, using the Spanish version of the DISCERN tool - a validated questionnaire designed to assess the quality and reliability of web-based information on treatment choices (rating scores from 15 to 75).

RESULTS

DISCERN scores given by parents and experts were low (total mean scores [standard deviation]: 35.9 [13.1] and 43.4 [13.7], respectively) and inter-rater agreement was poor/moderate (weighted kappa for the global assessment between -0.69 and +0.93, average = 0.29). There was a significant change on the ADHD-knowledge and motivation for treatment (ADHD-KMT) basic knowledge sub-scale score after the assessment of the different websites by parents (total mean scores [standard deviation]: 49.09 [9.46] and 63.21 [9.45]).

CONCLUSIONS

Despite a poor/moderate inter-rater agreement between parent and expert opinions, all agreed that the quality of the web-based information on treatment choices for ADHD is generally poor.

The viral transactivator HBx protein exhibits a high potential for regulation via phosphorylation through an evolutionarily conserved mechanism

BACKGROUND

Hepatitis B virus (HBV) encodes an oncogenic factor, HBx, which is a multifunctional protein that can induce dysfunctional regulation of signaling pathways, transcription, and cell cycle progression, among other processes, through interactions with target host factors. The subcellular localization of HBx is both cytoplasmic and nuclear. This dynamic distribution of HBx could be essential to the multiple roles of the protein at different stages during HBV infection. Transactivational functions of HBx may be exerted both in the nucleus, via interaction with host DNA-binding proteins, and in the cytoplasm, via signaling pathways. Although there have been many studies describing different pathways altered by HBx, and its innumerable binding partners, the molecular mechanism that regulates its different roles has been difficult to elucidate.

METHODS

In the current study, we took a bioinformatics approach to investigate whether the viral protein HBx might be regulated via phosphorylation by an evolutionarily conserved mechanism.

RESULTS

We found that the phylogenetically conserved residues Ser25 and Ser41 (both within the negative regulatory domain), and Thr81 (in the transactivation domain) are predicted to be phosphorylated. By molecular 3D modeling of HBx, we further show these residues are all predicted to be exposed on the surface of the protein, making them easily accesible to these types of modifications. Furthermore, we have also identified Yin Yang sites that might have the potential to be phosphorylated and O-β-GlcNAc interplay at the same residues.

CONCLUSIONS

Thus, we propose that the different roles of HBx displayed in different subcellular locations might be regulated by an evolutionarily conserved mechanism of posttranslational modification, via phosphorylation.

An epigenetic model for pigment patterning based on mechanical and cellular interactions

Pigment patterning in animals generally occurs during early developmental stages and has ecological, physiological, ethological, and evolutionary significance. Despite the relative simplicity of color patterns, their emergence depends upon multilevel complex processes. Thus, theoretical models have become necessary tools to further understand how such patterns emerge. Recent studies have reevaluated the importance of epigenetic, as well as genetic factors in developmental pattern formation. Yet epigenetic phenomena, specially those related to physical constraints that might be involved in the emergence of color patterns, have not been fully studied. In this article, we propose a model of color patterning in which epigenetic aspects such as cell migration, cell-tissue interactions, and physical and mechanical phenomena are central. This model considers that motile cells embedded in a fibrous, viscoelastic matrix-mesenchyme-can deform it in such a way that tension tracks are formed. We postulate that these tracks act, in turn, as guides for subsequent cell migration and establishment, generating long-range phenomenological interactions. We aim to describe some general aspects of this developmental phenomenon with a rather simple mathematical model. Then we discuss our model in the context of available experimental and morphological evidence for reptiles, amphibians, and fishes, and compare it with other patterning models. We also put forward novel testable predictions derived from our model, regarding, for instance, the localization of the postulated tension tracks, and we propose new experiments. Finally, we discuss how the proposed mechanism could constitute a dynamic patterning module accounting for pattern formation in many animal lineages.

Simultaneous nitrate and organic matter removal from salmon industry wastewater: the effect of C/N ratio, nitrate concentration and organic load rate on batch and continuous process

Although simultaneous denitrification-anaerobic digestion has been studied extensively, the use of salmon effluents as organic matter source has received little attention. This study evaluated the effect of C/N ratio, nitrate concentration, and organic load rate (OLR) on simultaneous nitrate and organic matter removal using salmon effluents. The study was carried out in a batch reactor with suspended biomass at 37 °C and pH 7.5, and in continuous biofilm tubular reactors at 37 °C fed with a mixture of a synthetic substrate and a saline protein-rich salmon-plant effluent. The results of the batch and continuous experiments showed that nitrate abatement was greater than 95% at all the studied C/N ratios, without effect of the C/N ratio on NO(3)(-)-N transformation and ammonia production. An increase of nitrate concentration increased organic matter consumption as well as the hydrolytic rate. The organic matter reduction varied between 88% and 40% in the continuous process. For a continuous process, the increase of the OLR decreases the removal of organic matter.

Test de atención D2: Datos normativos y desarrollo evolutivo de la atención en educación primaria

El objetivo de este trabajo ha sido analizar el desarrollo evolutivo de la atención y obtener datos normativos de la prueba de atención d2 en escolares de Educación Primaria (EP). Con este propósito se ha seleccionado una muestra de 1.032 alumnos escolarizados desde primero hasta sexto curso de EP en la Comunidad Autónoma de Canarias, con edades comprendidas entre los 6 años y 3 meses y los 12 años y 4 meses. En cuanto a la variable edad se analizaron los cambios que se observan con el paso de los años en las variables que mide el d2. Los resultados encontrados ponen de manifiesto la existencia de cambios significativos en las variables de productividad y efectividad, y no así en la medida de errores. Asimismo, se han calculado los percentiles correspondientes a cada una de las medidas del d2 para cada rango de edad.

Datos normativos para el test de Span Visual: estudio evolutivo de la memoria de trabajo visual y la memoria de trabajo verbal

El objetivo central del presente trabajo ha sido la baremación en una amplia muestra de población infantil de una prueba destinada a la evaluación de la memoria de trabajo visual. Además, hemos abordado el estudio del desarrollo evolutivo de la memoria de trabajo verbal y la memoria de trabajo visual. Se seleccionó a una muestra de 1.030 sujetos con edades comprendidas entre los 6 años y 3 meses y los 12 años y 4 meses que cursaban entre primero y sexto de educación primaria. Las pruebas utilizadas fueron: el Span Visual de la Wechsler Memory Scale, tanto en su versión directa como inversa, para la memoria de trabajo visual y la adaptación al español de la prueba de Memoria de Frases de Siegel y Ryan para la memoria de trabajo verbal. Los resultados encontrados ponen de manifiesto una mejora progresiva en el rendimiento en función de la edad en ambas pruebas. Se presentan tablas de medias, desviación estándar y percentiles para los distintos grupos de edad. Estos datos podrán ser utilizados como referencia normativa por aquellos profesionales interesados en el estudio del funcionamiento ejecutivo de la población escolar infantil.

Torre de Hanoi: datos normativos y desarrollo evolutivo de la planificación

El objetivo de este trabajo ha sido evaluar el desarrollo evolutivo de la planificación y obtener datos normativos de la prueba de planificación “Torre de Hanoi” en escolares de Educación Primaria (EP). Con este propósito se ha seleccionado una muestra de 1.032 alumnos/as escolarizados desde primero hasta sexto curso de EP en la Comunidad Autónoma de Canarias, con edades comprendidas entre los 6 años y 3 meses y los 12 años y 4 meses. Se analizó el número de diseños correctamente realizados por los escolares en los diferentes cursos. Los resultados encontrados ponen de manifiesto la existencia de tres momentos diferenciados en el desarrollo de la planificación, observándose un rendimiento inferior del alumnado de primer curso frente al resto de los cursos y un rendimiento más similar entre, por un lado, el alumnado de segundo, tercero y cuarto, y, por otro lado, entre el de quinto y sexto curso. Asimismo, se observa una mejora progresiva en la planificación -en función de la edad. Por último, se presenta el baremo para EP de la prueba “Torre de Hanoi”.

Datos normativos para el Test de los Cinco Dígitos: desarrollo evolutivo de la flexibilidad en Educación Primaria

El objetivo de este trabajo ha sido evaluar el desarrollo evolutivo de flexibilidad cognitiva y obtener datos normativos de la prueba “Test de los Cinco Dígitos” en escolares de Educación Primaria (EP) en la Comunidad Autónoma de Canarias. Con este propósito se seleccionó una muestra de 1.032 alumnos escolarizados entre primero y sexto curso de EP, con edades comprendidas entre los 6 y 12 años. Se analizó el tiempo invertido en la realización de las tareas de lectura, conteo y alternancia y calculándose finalmente el de flexibilidad. Los resultados encontrados ponen de manifiesto una tendencia lineal en el desarrollo de esta función, produciéndose un mayor crecimiento entre los 6 y 9 años y un descenso en la tasa de crecimiento entre los 9 y 13 años. Se calcularon también los baremos por curso de la prueba en la población escolar seleccionada de la Comunidad Autónoma de Canarias.