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CitrusGenome: Applying User Centered Design for Evaluating the Usability of Genomic User Interfaces
No full textSeveral tools have been developed to extract knowledge from the vast amount of data in genomics. The success of the knowledge extraction process depends to arge extent on how easy to learn and use are the tools for bioinformaticians. User interface design is neglected frequently in the genomic tool development process. As a result, user interfaces contain usability problems that make knowledge extraction a complex task. User-Centered Design (UCD) is a design approach that can be applied to improve the usability of interfaces. A fundamental principle of UCD is to design the UI based on users’ knowledge, their needs, objectives, and tasks to ensure that the resulting user interface meets the real user needs. We apply the UCD approach to design, evaluate and improve CitrusGenome, a tool that enables bioinformaticians to extract knowledge from genomic data. Following the UCD process, we first conduct user research to define user needs by applying UCD techniques such as interviews and task analysis. Then, we design a user interface that meets those user needs by using GenomIUm. GenomIUm is a systematic method that guides the design process of user interfaces in the genomic domain. We have performed two UCD iterations and, after each iteration, the user interfaces were validated by bioinformaticians. Some usability problems were found in each iteration. Therefore, we refined the user interface by solving the usability problems and incorporating such solutions into the final design. Finally, bioinformaticians using the refined user interface reported a reduction in the complexity of extracting knowledge from genomic data. We conclude that UCD techniques, together with GenomIUm, can be a useful strategy to design user interfaces that are easier to learn and use in the genomic domai
Modeling the Spatial Distribution of Xylella fastidiosa: A Nonstationary Approach with Dispersal Barriers
Get PDFSpatial species distribution models often assume isotropy and stationarity, implying that spatial dependence is direction-invariant and uniform throughout the study area. However, these assumptions are violated when dispersal barriers are present. Despite this, the issue of nonstationarity has been little explored in the context of plant health. The objective of this study was to evaluate the influence of barriers in the distribution of Xylella fastidiosa in the demarcated area in Alicante, Spain. Occurrence data from 2018 were analyzed through spatial Bayesian hierarchical models. The stationary model, illustrating a scenario without control interventions or geographical features, was compared with three nonstationary models: a model with mountains as physical barriers, and two models with a continuous and discontinuous perimeter barrier representing hypothetical control interventions. In the stationary model, the posterior mean of the spatial range, as the distance where two observations are uncorrelated, was 4,030 m 95% credible interval (2,907 to 5,564). This distance can be used to define the buffer zone in the demarcated area. The predicted probability of X. fastidiosa presence in the area outside the barrier was 0.46 with the stationary model, whereas it was reduced to 0.29 and 0.36 with the continuous and discontinuous barrier models, respectively. Differences between the discontinuous and continuous barrier models showed that breaks, where no control interventions were implemented, resulted in a higher predicted probability of X. fastidiosa presence in the areas with low sampling intensity. These results may help authorities prioritize the areas for surveillance and disease control
High-Throughput Sequencing Discloses the Cucumber Mosaic Virus (CMV) Diversity in Slovakia and Reveals New Hosts of CMV from the Papaveraceae Family
Get PDFCucumber mosaic virus (CMV; Cucumovirus, Bromoviridae) is an omnipresent virus characterized by a large host range and high genetic variability. Using high-throughput sequencing, we have characterized near complete genomes of 14 Slovak CMV variants from different plant hosts. Of these, three variants originated from the Papaveraceae species (oilseed poppy, common poppy and great celandine), previously poorly described as CMV natural hosts. Based on a BLAST search and phylogenetic analysis, the Slovak CMV isolates can be divided into two genetically different Groups, Ia and II, respectively. The SL50V variant, characterized by a divergent RNA2 sequence, potentially represents a reassortant variant. In four samples (T101, SL50V, CP2, MVU2-21), the presence of satellite CMV RNA was identified along with CMV. Although mechanically transmitted to experimental cucumber plants, the role of satellite RNA in the symptomatology observed could not be established due to a complex infection of original hosts with different viruses
Near infrared techniques applied to analysis of wheat-based products: Recent advances and future trends
Get PDFWheat flour is a food ingredient used in different processed food products, including pasta, cake, bread, among others. Therefore, the authentication and assurance of good quality are of great importance. Traditional techniques used for quality parameters determinations are laborious, destructive, and demand chemical analysis. Hence, it is necessary the development of techniques capable to overcome these disadvantages. Spectral techniques are rapid, non-destructive, and chemical-free. This review approaches the applications of Near Infrared (NIR) Spectroscopy, Fourier Transform Near-Infrared (FT-NIR) Spectroscopy, and Hyperspectral Imaging (HSI) in wheat flour and wheat-based products authentication and assessment of quality parameters, composition, and contamination. Considering the need from the processing industry for a rapid analysis, moving the bench-top analytical system to the production line, future studies can explore in/on-line applications of these techniques for industrial processing lines and compare the use of handheld and benchtop spectrometers in these applications
Selección genética de caracteres de interés en Nesidiocoris tenuis Reuter (Hemiptera: Miridae)
Get PDFNesidiocoris tenuis Reuter (Hemiptera: Miridae) es un depredador zoofitófago ampliamente utilizado en programas de control biológico en el cultivo de tomate en el sureste español. Debido a su amplia polifagia, este mírido permite un control eficaz de plagas clave, como Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) o Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae). Sin embargo, debido a su comportamiento fitófago, N. tenuis puede dañar gravemente las plantas de tomate cuando el nivel de presas es escaso
Liberación de machos estériles de Ceratitis capitata Wiedemann (Diptera: Tephritidae) como vectores de enfermedad causada por hongos entomopatógenos sobre las poblaciones silvestres
Get PDFDesde el año 2007, la Técnica del Insecto Estéril (TIE) es el principal medio de lucha del Plan de Acción de la Conselleria de Agricultura contra la mosca mediterránea de la fruta Ceratitis capitata Wiedemann (Diptera: Tephritidae) en la Comunitat Valenciana. Esta técnica consiste en la cría masiva de insectos macho de la misma especie a combatir que, tras ser esterilizados, se liberan al campo en grandes cantidades para que copulen con las hembras silvestres, siendo los huevos puestos por éstas infértiles
Búsqueda de interactores para la caracterización de los genes ParPMC implicados en la resistencia a Sharka en albaricoquero
Get PDFLa enfermedad de la Sharka, causada por el potyvirus Plum pox virus (PPV) es el factor más limitante para el cultivo de frutales de hueso. El desarrollo de variedades resistentes se ha propuesto como la mejor solución para el control de esta enfermedad. Sin embargo, se conocen pocas fuentes de resistencia que puedan ser de utilidad para su incorporación a los programas de mejora. En el caso de albaricoque se identificaron una decena de variedades norteamericanas que muestran resistencia a PPV. Combinando datos genéticos y genómicos propusimos a los genes ParPMC1 y ParPMC2 como genes de susceptibilidad cuyo silenciamiento confiere resistencia a PPV
Ralstonia solanacearum Facing Spread-Determining Climatic Temperatures, Sustained Starvation, and Naturally Induced Resuscitation of Viable but Non-Culturable Cells in EnvironmentalWater
Get PDFRalstonia solanacearum is a bacterial phytopathogen affecting staple crops, originally from tropical and subtropical areas, whose ability to survive in temperate environments is of concern under global warming. In this study, two R. solanacearum strains from either cold or warm habitats were stressed by simultaneous exposure to natural oligotrophy at low (4°C), temperate (14°C), or warm (24°C) temperatures in environmental water. At 4°C, the effect of temperature was higher than that of oligotrophy, since R. solanacearum went into a viable but non-culturable (VBNC) state, which proved to be dependent on water nutrient contents. Resuscitation was demonstrated in vitro and in planta. At 14°C and 24°C, the effect of oligotrophy was higher than that of temperature on R. solanacearum populations, displaying starvation-survival responses and morphological changes which were stronger at 24°C. In tomato plants, starved, cold-induced VBNC, and/or resuscitated cells maintained virulence. The strains behaved similarly regardless of their cold or warm areas of origin. This work firstly describes the natural nutrient availability of environmental water favoring R. solanacearum survival, adaptations, and resuscitation in conditions that can be found in natural settings. These findings will contribute to anticipate the ability of R. solanacearum to spread, establish, and induce disease in new geographical and climatic areas
Effect of Pulp Pigmentation Intensity on Consumer Acceptance of New Blood Mandarins: A Cross-Cultural Study in Spain and Italy
Get PDFOne of the current objectives of different citrus breeding programmes is obtaining new pigmented mandarins. This study investigates to what extent consumer preferences, expectations and purchase intention are affected by the appearance of new mandarins, specifically pulp pigmentation intensity. Four hundred consumers from both Italy and Spain (800 in all) participated in the study. In each country, half were informed about the healthy properties of the anthocyanins responsible for red pulp colouration, while the other half were not. Italians more readily accepted new mandarin varieties than Spaniards, which was linked to them being more familiar with blood oranges. In Italy, both slight-and medium-pigmented mandarins were well-accepted. Spanish consumers preferred the slight-pigmented variety. The most intense pigmented varieties were not well-accepted in either country. Health-related information positively affected Spaniards’ consumer response but did not modify that of Italians. A halo effect was detected in Spain, where health-related information positively affected mandarin appearance liking and its expected taste liking. Consumer perception that new varieties were unnatural was identified as a consumption barrier, mainly in Spain. Blood orange familiarity and health claims are revealed as conditioning factors for consumer response to pigmented mandarins. Interventions should be made to inform consumers that these varieties are obtained by conventional breeding and not by transgenic technology. Future studies should evaluate consumer response to other sensory characteristics, such as odour, taste and texture
Susceptibility of different prunus rootstocks to natural infection of plum pox virus-Turkey (PPV-T) in Central Anatolia
Get PDFSharka is the most damaging viral disease of Prunus spp. and the causative agent is plum pox virus (PPV). PPV is widespread and poses a serious problem in stone fruit crops in Turkey. A unique strain of PPV has so far been identified in Turkey and called as PPV-Turkey (PPV-T). The aims of the present study were to describe the efficiency of PPV-T transmission via aphids and to identify the susceptibility of different Prunus rootstocks against PPV-T strain under natural inoculum in Kayseri province located Central Anatolia Region of Turkey. This experiment was established in a small residential orchard where PPV-T infected apricot and plum trees were detected. Five different Prunus rootstocks from which 200 individuals were planted in PPV-T infected orchard and experiment was designed in a randomized complete block desing with 10 replications per block. All rootstocks were regularly tested by DAS-ELISA and RT-PCR during 2015–2017. The results showed that the most susceptible rootstocks in terms of PPV-T infection were Nemaguard, Myrobalan 29B and Myrobalan 29C with the infection rate of 3.61%, 2.74% and 1.04%, respectively. On the other hand, GF677 and Garnem were never found infected with PPV-T. Aphis gossypii, A. craccivora, A. spiraecola, Brachycaudus helichrysi, Hyalopterus pruni, Myzus persicae, Macrosiphum euphorbiae were detected as most abundant aphid species in experimental plot. In 2015, the highest percentage of viruliferous aphids was found as A. gossypii (100%), followed by B. helichrysi (77.8%), A. spiraecola (55.72%), M. persicae (46.05%) and H. pruni (30.76%) whereas it was 100% for A. gossypii and M. euphorbiae followed by A. spiraecola (76.32%), M. persicae (73.1%), H. pruni (62.06%) and B. helichrysi (61.53%) in 2016 by squash real time RT-PCR. The present study showed that PPV-T was effectively transmitted by different aphid species in natural conditions in Kayseri district. It was concluded that Nemaguard and Myrobalan which were found to be the most sensitive rootstocks to PPV-T should not be preferred by growers as Prunus rootstock where PPV poses a high risk