Search results for "Analysis tools"
showing 10 items of 22 documents
On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
2020
Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of commo…
Increase in gut microbiota after immune suppression in baculovirus-infected larvae.
2013
Spodoptera exigua microarray was used to determine genes differentially expressed in S. exigua cells challenged with the species-specific baculovirus SeMNPV as well as with a generalist baculovirus, AcMNPV. Microarray results revealed that, in contrast to the host transcriptional shut-off that is expected during baculovirus infection, S. exigua cells showed a balanced number of up- and down-regulated genes during the first 36 hours following the infection. Many immune-related genes, including pattern recognition proteins, genes involved in signalling and immune pathways as well as immune effectors and genes coding for proteins involved in the melanization cascade were found to be down-regul…
Analyzing Illumina Gene Expression Microarray Data from Different Tissues: Methodological Aspects of Data Analysis in the MetaXpress Consortium
2012
Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data preprocessing and the variability due to sample processing in whole blood cell and blood monocyte gene expression data, measured on the Illumina HumanHT-12 v3 BeadChip array. Gene expression signal intensities were similar after applying the log(2) or the variance-stabilizing transformation. In all cohorts, the first principal component (PC) explained more than 95% of the total variation. Technic…
Listeria monocytogenes Differential Transcriptome Analysis Reveals Temperature-Dependent Agr Regulation and Suggests Overlaps with Other Regulons
2012
Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its Delta agrA mutant at the saprophytic temperature of 25 degrees C and in vivo temperature of 37 degrees C. Variations of transcriptome were higher at 37 degrees C than at 25 degrees C. Results suggested that AgrA may be involved in the regu…
Developing Phonological Awareness in Blended-learning Language Courses
2013
This study is based on Second Language Acquisition through blended learning and explores the application of new educational technologies in the development of distance education. In particular, the paper focuses on ways to enhance oral, aural, and intercultural skills through learners' engagement, develop authentic social interaction and intercultural awareness in virtual environments and at the same time actively engage the students' powers of perception, communication DQGUHDVRQLQJ��$ �VSHHFKYLVXDOL) DWLRQWHFKQRORJ\ �LVLQWURGXFHG�� VSHFL?FDOO\�WDLO RUHGWR� pronunciation training. It provides relevant and comprehensible visual feedback of all three components of speech: prosody-intonation, …
Neutrino oscillation probabilities through the looking glass
2019
In this paper we review different expansions for neutrino oscillation probabilities in matter in the context of long-baseline neutrino experiments. We examine the accuracy and computational efficiency of different exact and approximate expressions. We find that many of the expressions used in the literature are not precise enough for the next generation of long-baseline experiments, but several of them are while maintaining comparable simplicity. The results of this paper can be used as guidance to both phenomenologists and experimentalists when implementing the various oscillation expressions into their analysis tools.
Strategic Analysis Tools Application at SMEs in Ecuador
2015
This article explores the nature and scope of Strategic Analysis Tools (SAT) application in SMEs located in emerging countries such as Ecuador (where there are no formal studies on the subject). It is intended to assess which of the instruments utilized by these firms may contribute to formulate strategic options and which of them create awareness of relevant risks or distress specifically about continuity concerning their operations. Through the application of a survey to an intentional sample-selection of SMEs in Quito-Ecuador we analyzed the consciousness over these instruments to facilitate the creation of strategic options, their contribution to assess their competitive position and th…
Simple Strategic Analysis Tools at SMEs in Ecuador
2015
This article explores the possible applications of Strategic Analysis Tools (SAT) in SMEs located in emerging countries such as Ecuador (where there are no formal studies on the subject). It is intended to analyze if whether or not it is feasible to effectively apply a set of proposed tools to guide mental map decisions of executives when decisions on strategy have to be made. Through an in-depth review of the state of the art in regards to SAT and interviews performed to main participants such as chambers and executives of different firms, it is shown the feasibility of their application. This analysis is complemented with specialists´ interviews to deepen our insights and obtaining valid …
Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
2013
Neuroblastoma is an embryonic tumor arising from immature sympathetic nervous system cells. Recurrent genomic alterations include MYCN and ALK amplification as well as recurrent patterns of gains and losses of whole or large partial chromosome segments. A recent whole genome sequencing effort yielded no frequently recurring mutations in genes other than those affecting ALK. However, the study further stresses the importance of DNA copy number alterations in this disease, in particular for genes implicated in neuritogenesis. Here we provide additional evidence for the importance of focal DNA copy number gains and losses, which are predominantly observed in MYCN amplified tumors. A focal 5 kb…
High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.).
2011
14 páginas, 5 figuras, 3 tablas, S4 figuras, S2 tablas