Towards a Robust Method of Modelling Leaf Appearance in Plants

The thermal interval for leaf tip appearance (phyllochron) is a critical variable for modelling plant development and growth. Phyllochron varies across environments, but is generally constant for a species grown in specific environments. For example, the phyllochron in maize is lower in temperate environments than in tropical and subtropical environments. The limitation of existing data is that each experiment has been evaluated in a narrow range of environments, and underlying mechanisms have not been adequately examined. Consequently, no method is available to model the variation across environments. Models use constant values that are fixed for particular environments. This situation is unsatisfactory, as model users must have values that have been determined for their locality. A method of adjusting the value of phyllochron according to genotype adaptation groups or environmental conditions is required. Of these two options, the latter appears most promising as there is little, if any, variation among genotypes when grown in specific environments. Recent information shows that phyllochron in maize is related to light intensity. The data also suggests that phyllochron depends on the adequacy of current photosynthesis (source) to meet the demands of the plant for growth (sink), one aspect of which is the production of new leaves. This paper reports on concepts and early progress in relating phyllochron to both irradiance and thermal time

Development of an online computational platform for the analysis of protein synthesis and detection of novel translated regions

Ribosome profiling is a technique that allows us to capture and sequence mRNA fragments protected by ribosome complexes. Mapping these ribosome protected fragments or RPFs, back to a genome or transcriptome provides information on the precise location of elongating ribosomes. This data can then be used to detect novel translated regions, translational pausing and differentially translated genes. Chapter 2 describes the development of Trips-Viz, an interactive online platform for the exploration and visualisation of RPFs mapped to the transcriptomes of various different organisms. This allows users to rapidly aggregate and visualise ribosome profiling data at a single transcript level allowing for visual detection of translated open reading frames. Trips-Viz also allows users to rapidly assess the quality of data through various meta-information plots as well as detect and visualise transcripts that are differentially expressed/translated between two conditions. These analyses can be carried out through a GUI, meaning users do not need any prior coding or command line experience to be able to use them. Chapter 3 describes the major updates made to Trips-Viz since its original publication. This includes the addition of mass spectrometry data. Several thousand human mass spectrometry datasets have been processed and detected peptides mapped to the human transcriptome in the same manner as ribosome profiling data. This allows users to corroborate the evidence from the ribosome profiling data and provides information on whether a translated ORF is capable of producing a stable protein product. The differential expression/translation detection has also been improved with the inclusion of the Deseq2 and Anota2seq software. A method for the automatic detection of translated ORFs was also included which allows users to find translated uORFs, nested ORFs, downstream ORFs in a relatively timely manner. Other improvements include the addition of help videos to guide users through the navigation and interacting with the users interface of Trips-Viz. Finally, incorporating the relevant scripts into RiboGalaxy made it easier for users to upload their own data and transcriptomes to Trips-Viz without any requirement for command line expertise

Contracts in Practice

Contracts are a form of lightweight formal specification embedded in the program text. Being executable parts of the code, they encourage programmers to devote proper attention to specifications, and help maintain consistency between specification and implementation as the program evolves. The present study investigates how contracts are used in the practice of software development. Based on an extensive empirical analysis of 21 contract-equipped Eiffel, C#, and Java projects totaling more than 260 million lines of code over 7700 revisions, it explores, among other questions: 1) which kinds of contract elements (preconditions, postconditions, class invariants) are used more often; 2) how contracts evolve over time; 3) the relationship between implementation changes and contract changes; and 4) the role of inheritance in the process. It has found, among other results, that: the percentage of program elements that include contracts is above 33% for most projects and tends to be stable over time; there is no strong preference for a certain type of contract element; contracts are quite stable compared to implementations; and inheritance does not significantly affect qualitative trends of contract usage

Advancement of a Soil Parameters Geodatabase for the Modeling Assessment of Conservation Practice Outcomes in the United States

US-ModSoilParms-TEMPLE is a database composed of a set of geographic databases functionally storing soil-spatial units and soil hydraulic, physical, and chemical parameters for three agriculture management simulation models, SWAT, APEX, and ALMANAC. This paper introduces the updated US-ModSoilParms-TEMPLE, which covers the entire United States and is organized as a framework of 22 nested and hydrologically-ordered regional geographic databases with internal spatial segmentation drainage-defined at a conveniently manageable tile (Watershed Boundary Dataset’s, WBD, 8-digit Subbasin) level. Spatial features are stored in multiple formats (raster and vector) and resolutions (10-meter and 30-meter), while being in direct relationship with the table of attributes storing the models’ parameters. A significant number of former parameter voids, determined by the local incompleteness of the source datasets, were filled using a methodology leveraging upon the hierarchy of the Soil Taxonomy information and the geographic location of the gaps. The functionality of each geographic database was extended by adding customized tools, which streamline the incorporation into geoprocessing workflows, the aggregation and extraction of data sets, and finally the export to other model support software user environments. These tools are attached and conveniently distributed along with detailed metadata documentation within each of the developed regional geographic databases. The system hosting this framework is developed using a proprietary software format (ESRI® File Geodatabase), however, a companion version of the framework of 8-digit tiles is also developed and provided using openly accessible formats. The experience shared in this paper might help other efforts in developing hydrology-oriented geographical databases

Similarity of maize seed number responses for a diverse set of sites

Accurate modeling of maize (Zea mays L.) yields in diverse environments requires realistic simulation of seed numbers. Response of maize seed number to growth or light interception soon after pollination has been described with different types of functions. The objective of this study was to compare maize seed number responses to intercepted solar radiation or growth with data from a diverse set of sites. Pioneer hybrid 3394 planted near Temple, TX in 1999 at 2.5 to 20 plants$\cdot$m$^{-2}$ showed a linear function for seed number responses to light intercepted per plant in the 11 d following silking and to ear growth rate in these 11 d. Similar linear seed number responses were found for three hybrids in Canada at 4 to 13 plants$\cdot$m$^{-2}$. Likewise, the function for Pioneer 3394 in Temple was found to be similar to a regression for the same hybrid grown in Pennsylvania, and was similar to a function developed in Kenya. Thus, under the diverse environmental conditions of these studies, linear seed number functions appeared reasonable at these sites. Such seed number functions are critical to the understanding of optimization of planting density to maximum seed production per unit ground area. In the absence of drought stress, the optimum density will be the minimum planting density which could attain near-complete light interception at silking. As the probability of drought stress increases due to decreased soil water holding capacity or decreased expected rainfall, the optimum density would decrease accordingly.Similarité des réponses du nombre de grains par épi de maïs pour un jeu de sites variés. La modélisation précise des rendements du maïs (Zea mays L.) dans divers environnements nécessite une simulation réaliste du nombre de grains par épi. La réponse du nombre de grains à la croissance ou à l'interception de la lumière aussitôt après la pollinisation a été décrite avec différents types de fonctions. L'objectif de cette étude était de comparer les réponses du nombre de grains par épi au rayonnement solaire intercepté ou à la croissance de l'épi avec les données provenant d'un ensemble de sites variés. L'hybride Pioneer 3394 planté près de Temple (Texas, USA) en 1999 avec 2,5 à 20 plants$\cdot$m$^2$ a montré une relation linéaire entre le nombre de grains et la lumière interceptée durant les 11 jours qui ont suivi la sortie des soies ainsi qu'avec le taux de croissance de l'épi durant ces mêmes 11 jours. Des réponses linéaires similaires ont été trouvées pour trois hybrides au Canada avec 4 à 13 plants$\cdot$m$^2$. De même, la relation pour Pioneer 3394 à Temple a été trouvée similaire à celle obtenue pour le même hybride cultivé en Pennsylvanie ainsi qu'au Kenya. Ainsi, sous diverses conditions d'environnement de ces études, une relation linéaire avec le nombre de grains apparaît comme raisonnable dans ces sites. De telles relations linéaires avec le nombre de grains sont critiques pour appréhender l'optimisation de la densité de plantation afin d'atteindre le maximum de production de grains par unité de surface de sol. En l'absence de stress dû à la sécheresse, la densité optimale sera la densité de plantation minimale qui permettrait d'atteindre l'interception pratiquement complète du rayonnement au moment de la sortie des soies. Comme la probabilité de stress hydrique augmente avec la décroissance de la capacité de rétention en eau du sol ou décroît avec les précipitations escomptées, la densité optimale devra décroître en tenant compte de ces facteurs

GWIPS-viz: 2018 update

The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome

The GWIPS-viz browser

GWIPS-viz is a publicly available browser that provides Genome Wide Information on Protein Synthesis through the visualization of ribosome profiling data. Ribosome profiling (Ribo-seq) is a high-throughput technique which isolates fragments of messenger RNA that are protected by the ribosome. The alignment of the ribosome-protected fragments or footprint sequences to the corresponding reference genome and their visualization using GWIPS-viz allows for unique insights into the genome loci that are expressed as potentially translated RNA. The GWIPS-viz browser hosts both Ribo-seq data and corresponding mRNA-seq data from publicly available studies across a number of genomes, avoiding the need for computational processing on the user side. Since its initial publication in 2014, over 1885 tracks have been produced across 24 genomes. This unit describes the navigation of the GWIPS-viz genome browser, the uploading of custom tracks, and the downloading of the Ribo-seq/mRNA-seq alignment data

TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response

Translation initiation is the rate-limiting step of protein synthesis that is downregulated during the Integrated Stress Response (ISR). Previously, we demonstrated that most human mRNAs that are resistant to this inhibition possess translated upstream open reading frames (uORFs), and that in some cases a single uORF is sufficient for the resistance. Here we developed a computational model of Initiation Complexes Interference with Elongating Ribosomes (ICIER) to gain insight into the mechanism. We explored the relationship between the flux of scanning ribosomes upstream and downstream of a single uORF depending on uORF features. Paradoxically, our analysis predicts that reducing ribosome flux upstream of certain uORFs increases initiation downstream. The model supports the derepression of downstream translation as a general mechanism of uORF-mediated stress resistance. It predicts that stress resistance can be achieved with long slowly decoded uORFs that do not favor translation reinitiation and that start with initiators of low leakiness

Computational methods for ribosome profiling data analysis

Since the introduction of the ribosome profiling technique in 2009 its popularity has greatly increased. It is widely used for the comprehensive assessment of gene expression and for studying the mechanisms of regulation at the translational level. As the number of ribosome profiling datasets being produced continues to grow, so too does the need for reliable software that can provide answers to the biological questions it can address. This review describes the computational methods and tools that have been developed to analyze ribosome profiling data at the different stages of the process. It starts with initial routine processing of raw data and follows with more specific tasks such as the identification of translated open reading frames, differential gene expression analysis, or evaluation of local or global codon decoding rates. The review pinpoints challenges associated with each step and explains the ways in which they are currently addressed. In addition it provides a comprehensive, albeit incomplete, list of publicly available software applicable to each step, which may be a beneficial starting point to those unexposed to ribosome profiling analysis. The outline of current challenges in ribosome profiling data analysis may inspire computational biologists to search for novel, potentially superior, solutions that will improve and expand the bioinformatician's toolbox for ribosome profiling data analysis