mRNAstab : a web application for mRNA stability analysis

Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of transcription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments

Genomic-scale analysis of DNA words of arbitrary length by parallel computation.

In the post-genomic era, one of the main tasks is deciphering the meaning of the DNA sequences of complex organisms. In order to do so, there is a clear need for biocomputer tools able to extract and order the information of long DNA molecules, such as whole chromosomes or even complete genomes. However, most genomic analyses have been concentrated on the detection and counting of short words having sizes of between 1 and 10 nucleotides. In this paper, we describe parallel algorithms with different complexities that exhaustively determine all words of size k, k being arbitrarily large, in a source DNA sequence. The results shown that our algorithms achieve a high degree of scalability, allowing the detection of DNA words of 64 nucleotides in only 800 seconds

A feedback mechanism controls rDNA copy number evolution in yeast independently of natural selection

Ribosomal DNA (rDNA) is the genetic loci that encodes rRNA in eukaryotes. It is typically arranged as tandem repeats that vary in copy number within the same species. We have recently shown that rDNA repeats copy number in the yeast Saccharomyces cerevisiae is controlled by cell volume via a feedback circuit that senses cell volume by means of the concentration of the free upstream activator factor (UAF). The UAF strongly binds the rDNA gene promoter, but is also able to repress SIR2 deacetylase gene transcription that, in turn, represses rDNA amplification. In this way, the cells with a smaller DNA copy number than what is optimal evolve to increase that copy number until they reach a number that sequestrates free UAF and provokes SIR2 derepression that, in turn, blocks rDNA amplification. Here we propose a mathematical model to show that this evolutionary process can amplify rDNA repeats independently of the selective advantage of yeast cells having bigger or smaller rDNA copy numbers. We test several variants of this process and show that it can explain the observed experimental results independently of natural selection. These results predict that an autoregulated feedback circuit may, in some instances, drive to non Darwinian deterministic evolution for a limited time period

Inference of the life cycle of environmental phages from genomic signature distances to their hosts

The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids

Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite

The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called 'RNASeq' and 'VariantSeq' to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, 'RNASeq' and 'VariantSeq' are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. 'RNASeq' and 'VariantSeq' are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. 'RNASeq' and 'VariantSeq' also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software

The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador

A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40  years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change

Soil Bacterial Community Along an Altitudinal Gradient in the Sumaco, a Stratovolcano in the Amazon Region

Our study is a pioneering exploration of the microbiome in the soil of the Sumaco stratovolcano and an assessment of the effects of an elevational gradient and related physicochemical soil parameters on richness and community structure. The Sumaco, as an isolated Amazonian stratovolcano, may be among one of the least studied ecosystems in Ecuador and perhaps the Amazon region. Universal patterns remain unresolved or available information inconclusive to establish a supported consensus on general governing processes by which elevation and its associated environmental gradients may determine the microbial richness and community structure. We tested a recent proposal on how microbial diversity responds to montane gradients, placing a central role in soils as potentially independent of altitude along an elevational gradient. Correlations and effects among soil physicochemical parameters and altitude were contrasted against richness and community structure through quantitative ecology. The most informative physicochemical parameter in our assessment of bacterial community structure was neither pH nor altitude, but sulfur, which was mostly independent of the other tested parameters. We established a positive effect of richness by parameters associated with metallic cations such as Mn2+, and CEC, which were negatively correlated to altitude and pH. The possible relation between the significant role of sulfur on bacterial community structure with the unique geological origin of the Sumaco stratovolcano should be examined in the context of specialized sulfur metabolisms and additional information on community structure and environmental constraints. Our study establishes an initial baseline for further explorations of microbial diversity in this unexplored tropical stratovolcano

La evaluación personalizada como estrategia de motivación

En el sistema educativo actual, es habitual que el estudiante concentre la mayor parte de su tiempo de estudio en las fechas cercanas a las pruebas de evaluación. Con el objetivo de fomentar el trabajo constante a lo largo del curso, exponemos una metodología docente basada en la evaluación continua y modelable por el alumno, que al mismo tiempo ayuda a evitar el plagio. Por un lado, los laboratorios se evalúan ‘in situ’ mediante una prueba que se realiza durante la sesión, en la que el alumno debe demostrar que ha preparado previamente la práctica y que ha realizado y entendido las actividades realizadas a lo largo de la sesión de laboratorio. Por el otro, en las clases de teoría y problemas, utilizamos trabajos voluntarios consistentes en problemas de dificultad variable y cuya evaluación puede, a elección del alumno, reducir de forma considerable el peso del examen final. Para fomentar el trabajo colaborativo, éstos pueden realizarse opcionalmente en grupo, aunque su corrección se realiza individualmente en horario de tutorías. Esta metodología ha sido utilizada exitosamente en dos asignaturas de la titulación de Ingeniería en Informática de la Universidad de Valencia. En el artículo se exponen los resultados académicos obtenidos, que respaldan su efectividad.In the current Higher Education system, it is common that students concentrate most of their effort close to the examination dates. In this paper we present a teaching methodology that aims at encouraging continuous work. To this end, an adaptive evaluation model has been used. This model inherently contributes to avoid plagiarism. On the one hand, computer labs are evaluated “in place”, by means of a test that students much complete at the end of each session. In this test, the student has to demonstrate that both the prelab work and the lab activities were appropriately done. On the other hand, voluntary course works are proposed during theoretical lectures. These consist of a collection of problems of variable difficulty. By handing their solution, students may considerably reduce the weight of the final exam. In addition, to encourage collaborative learning, these can be optionally solved in teams. Nevertheless, marking is always done individually, in tutorial hours. This methodology has been successfully applied in two modules of the Computer Science degree at the University of Valencia. This article presents the academic results that support its benefits.Los autores agradecen la financiación recibida desde el Vicerrectorado de Convergencia Europea y Calidad de la Universitat de València, a través de los proyectos DocenTIC y Finestra Oberta con códigos 08/DT/04/2009, 18/DT/05/2010 y 47/FO/35/2010; y desde el Ministerio de Educación y Ciencia y los fondos FEDER de la Comisión Europea, mediante los proyectos Consolider Ingenio 2010 CSD2007-00018 y CSD2006-00046, y el proyecto TIN2009-14475-C04

La Evalución personalizada como estrategia de motivación

En el sistema educativo actual, es habitual que el estudiante concentre la mayor parte de su tiempo de estudio en las fechas cercanas a las pruebas de evaluación. Con el objetivo de fomentar el trabajo constante a lo largo del curso, exponemos una metodología docente basada en la evaluación continua y modelable por el alumno, que al mismo tiempo ayuda a evitar el plagio. Por un lado, los laboratorios se evalúan ‘in situ’ mediante una prueba que se realiza durante la sesión, en la que el alumno debe demostrar que ha preparado previamente la práctica y que ha realizado y entendido las actividades realizadas a lo largo de la sesión de laboratorio. Por el otro, en las clases de teoría y problemas, utilizamos trabajos voluntarios consistentes en problemas de dificultad variable y cuya evaluación puede, a elección del alumno, reducir de forma considerable el peso del examen final. Para fomentar el trabajo colaborativo, éstos pueden realizarse opcionalmente en grupo, aunque su corrección se realiza individualmente en horario de tutorías. Esta metodología ha sido utilizada exitosamente en dos asignaturas de la titulación de Ingeniería en Informática de la Universidad de Valencia. En el artículo se exponen los resultados académicos obtenidos, que respaldan su efectividad.SUMMARY: In the current Higher Education system, it is common that students concentrate most of their effort close to the examination dates. In this paper we present a teaching methodology that aims at encouraging continuous work. To this end, an adaptive evaluation model has been used. This model inherently contributes to avoid plagiarism. On the one hand, computer labs are evaluated “in place”, by means of a test that students much complete at the end of each session. In this test, the student has to demonstrate that both the prelab work and the lab activities were appropriately done. On the other hand, voluntary course works are proposed during theoretical lectures. These consist of a collection of problems of variable difficulty. By handing their solution, students may considerably reduce the weight of the final exam. In addition, to encourage collaborative learning, these can be optionally solved in teams. Nevertheless, marking is always done individually, in tutorial hours. This methodology has been successfully applied in two modules of the Computer Science degree at the University of Valencia. This article presents the academic results that support its benefits.Peer Reviewe