Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-ble...
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Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching, and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. Here, we provide an overview of light sheet-based microscopy assays for in vitro and in vivo imaging of biological samples, including cell extracts, soft gels, and large multicellular organisms. We furthermore describe computational tools for basic image processing and data inspection. less
Complex networks with causal relationships among variables are pervasive in biology. Their study, however, requires special modeling approaches. Structural equation models (SEM) allow the representation of causal mech...
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Complex networks with causal relationships among variables are pervasive in biology. Their study, however, requires special modeling approaches. Structural equation models (SEM) allow the representation of causal mechanisms among phenotypic traits and inferring the magnitude of causal relationships. This information is important not only in understanding how variables relate to each other in a biological system, but also to predict how this system reacts under external interventions which are common in fields related to health and food production. Nevertheless, fitting a SEM requires defining a priori the causal structure among traits, which is the qualitative information that describes how traits are causally related to each other. Here, we present directions for the applications of SEM to investigate a system of phenotypic traits after searching for causal structures among them. The search may be performed under confounding effects exerted by genetic correlations. less
Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite f...
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Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs using deep sequencing data. less
In recent years R has become de facto statistical programming language of choice for statisticians and it is also arguably the most widely used generic environment for analysis of high-throughput genomic data. In this...
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In recent years R has become de facto statistical programming language of choice for statisticians and it is also arguably the most widely used generic environment for analysis of high-throughput genomic data. In this chapter we discuss some approaches to improve performance of R when working with large SNP datasets. less
This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a...
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This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a worked out example of QC pipeline starting with raw data and finishing with a fully filtered dataset ready for downstream analysis. The emphasis is on automation of data storage, filtering, and manipulation to ensure data integrity throughput the process and on how to extract a global summary from these high dimensional datasets to allow better-informed downstream analytical decisions. All examples will be run using the R statistical programming language followed by a practical example using a fully automated QC pipeline for the Illumina platform. less
Natural selection has molded the evolution of species across all taxa. Much more recently, on an evolutionary scale, human-oriented selection started to play an important role in shaping organisms, markedly so after t...
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Natural selection has molded the evolution of species across all taxa. Much more recently, on an evolutionary scale, human-oriented selection started to play an important role in shaping organisms, markedly so after the domestication of animals and plants. These selection processes have left traceable marks in the genome. Following from the recent advances in molecular genetics technologies, a number of methods have been developed to detect such signals, termed genomic signatures of selection. In this chapter we discuss a straightforward protocol based on the FST statistic to identify genomic regions that exhibit high variation in allelic frequency between groups, which is a characteristic of genomic regions that have gone through differential selection. How to define the borders of these regions and further explore its genetic content is then discussed. less
Plants accumulate an overwhelming variety of secondary metabolites that play important roles in defense and interaction of the plant with its environment. To investigate the dynamics of plant secondary metabolism, lar...
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Plants accumulate an overwhelming variety of secondary metabolites that play important roles in defense and interaction of the plant with its environment. To investigate the dynamics of plant secondary metabolism, large-scale untargeted metabolite profiling (metabolomics) is mandatory. Here, we describe a detailed protocol for untargeted metabolite profiling in which methanol extracts of jasmonate-treated plant tissues are analyzed by reversed-phase liquid chromatography coupled to negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (MS). By means of dedicated integration and alignment software, the relative abundance of thousands of mass peaks, corresponding to hundreds of compounds, is calculated, and mass peaks of which the area is significantly changed by jasmonate treatment are identified. Subsequently, the metabolites corresponding to the significantly changed peaks are tentatively annotated using the accurate mass prediction of the Fourier transform-MS and the generated MS/MS data. Via this method, compounds of medium polarity, such as glucosinolates, alkaloids, phenylpropanoids, flavonoids, polyamines, and saponins, can be analyzed. less
Software resources have the disadvantage that they are restricted to the most common applications. As a possible solution, universities have proposed to teach different programming languages for different learning str...
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Software resources have the disadvantage that they are restricted to the most common applications. As a possible solution, universities have proposed to teach different programming languages for different learning streams. This manuscript describes an early study about the optimal programming language for these studies. The results show that Visual Basic for Applications is the most adequate language. (C) 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 591-597, 2011;View this article online at ***/journal/cae;DOI 10.1002/cae.20339
Since years, multiple researches studied component-based software development. Nevertheless, most component-based software systems do not use components at implementation stage. We believe that one of the main causes ...
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Since years, multiple researches studied component-based software development. Nevertheless, most component-based software systems do not use components at implementation stage. We believe that one of the main causes is a lack of support for component-oriented programming (COP). Indeed, most of the proposed component models such as Unified Modeling language (UML), Corba Component Model (CCM), Enterprise Java Beans (EJB) are only available at design time. The fact that implementation relies on object-oriented languages which prevent developers from fully switching to COP. In this paper, we identify five important requirements (decoupling, adaptability, unplanned connections, encapsulation and uniformity) for COP based on an analysis of the state of the art and the limitations of existing work. We propose an extended version of the SCL component language that fulfills these requirements. A prototype of SCL and a concrete experiment validate this proposal. (C) 2011 Elsevier Ltd. All rights reserved.
At present, engineering students must learn an adequate programming language that allows them to easily automate typical problems. This result is more important when we require an adequate graphical representation of ...
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At present, engineering students must learn an adequate programming language that allows them to easily automate typical problems. This result is more important when we require an adequate graphical representation of the problem, as is usually done in engineering. This study presents an optimal programming language for quality control analysis. The results show that Visual Basic for Applications is the most adequate language that reduces the programming time;moreover, it is compatible with limited resources. (C) 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 20: 187-192, 2012;View this article online at ***/journal/cae;DOI 10.1002/cae.20384
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