Analyzing epigenomic data in a large-scale context

While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. In a typical analysis, users are required to download huge files that span the entire genome, even if they are only interested in a small subset (e.g., promoter regions) or an aggregation thereof. Moreover, complex operations on genome-level data are not always feasible on a local computer due to resource limitations. The DeepBlue Epigenomic Data Server mitigates this issue by providing a robust server that affords a powerful API for searching, filtering, transforming, aggregating, enriching, and downloading data from several epigenomic consortia. Furthermore, its main component implements scalable data storage and Manipulation methods that scale with the increasing amount of epigenetic data, thereby making it the ideal resource for researchers that seek to integrate epigenomic data into their analysis workflow. This work also presents companion tools that utilize the DeepBlue API to enable users not proficient in scripting or programming languages to analyze epigenomic data in a user-friendly way: (i) an R/Bioconductor package that integrates DeepBlue into the R analysis workflow. The extracted data are automatically converted into suitable R data structures for downstream analysis and visualization within the Bioconductor frame- work; (ii) a web portal that enables users to search, select, filter and download the epigenomic data available in the DeepBlue Server. This interface provides elements, such as data tables, grids, data selections, developed for empowering users to find the required epigenomic data in a straightforward interface; (iii) DIVE, a web data analysis tool that allows researchers to perform large-epigenomic data analysis in a programming-free environment. DIVE enables users to compare their datasets to the datasets available in the DeepBlue Server in an intuitive interface, which summarizes the comparison of hundreds of datasets in a simple chart. Furthermore, these tools are integrated, being capable of sharing results among themselves, creating a powerful large-scale epigenomic data analysis environment. The DeepBlue Epigenomic Data Server and its ecosystem was well received by the International Human Epigenome Consortium and already attracted much attention by the epigenomic research community with currently 160 registered users and more than three million anonymous workflow processing requests since its release.Während große Mengen epigenomischer Daten öffentlich verfügbar sind, ist ihre Abfrage in einer für die Downstream-Analyse geeigneten Form ein Engpass in der aktuellen Forschung. Bei einer typischen Analyse müssen Benutzer riesige Dateien herunterladen, die das gesamte Genom umfassen, selbst wenn sie nur an einer kleinen Teilmenge (z.B., Promotorregionen) oder einer Aggregation davon interessiert sind. Darüber hinaus sind komplexe Vorgänge mit Daten auf Genomebene aufgrund von Ressourceneinschränkungen auf einem lokalen Computer nicht immer möglich. Der DeepBlue Epigenomic Data Server behebt dieses Problem, indem er eine leistungsstarke API zum Suchen, Filtern, Umwandeln, Aggregieren, Anreichern und Herunterladen von Daten verschiedener epigenomischer Konsortien bietet. Darüber hinaus implementiert der DeepBlue-Server skalierbare Datenspeicherungs- und manipulationsmethoden, die der zunehmenden Menge epigenetischer Daten gerecht werden. Dadurch ist der DeepBlue Server ideal für Forscher geeignet, die die aktuellen epigenomischen Ressourcen in ihren Analyse-Workflow integrieren möchten. In dieser Arbeit werden zusätzlich Begleittools vorgestellt, die die DeepBlue-API verwenden, um Benutzern, die sich mit Scripting oder Programmiersprachen nicht auskennen, die Möglichkeit zu geben, epigenomische Daten auf benutzerfreundliche Weise zu analysieren: (i) ein R/ Bioconductor-Paket, das DeepBlue in den R-Analyse-Workflow integriert. Die extrahierten Daten werden automatisch in geeignete R-Datenstrukturen für die Downstream-Analyse und Visualisierung innerhalb des Bioconductor-Frameworks konvertiert; (ii) ein Webportal, über das Benutzer die auf dem DeepBlue Server verfügbaren epigenomischen Daten suchen, auswählen, filtern und herunterladen können. Diese Schnittstelle bietet Elemente wie Datentabellen, Raster, Datenselektionen, mit denen Benutzer die erforderlichen epigenomischen Daten in einer einfachen Schnittstelle finden können; (iii) DIVE, ein Webdatenanalysetool, mit dem Forscher umfangreiche epigenomische Datenanalysen in einer programmierungsfreien Umgebung durchführen können. Mit DIVE können Benutzer ihre Datensätze mit den im Deep- Blue Server verfügbaren Datensätzen in einer intuitiven Benutzeroberfläche vergleichen. Dabei kann der Vergleich hunderter Datensätze in einem Diagramm ausgedrückt werden. Aufgrund der großen Datenmenge, die in DIVE verfügbar ist, werden Methoden bereitgestellt, mit denen die ähnlichsten Datensätze für eine vergleichende Analyse vorgeschlagen werden können. Alle zuvor genannten Tools sind miteinander integriert, so dass sie die Ergebnisse untereinander austauschen können, wodurch eine leistungsstarke Umgebung für die Analyse epigenomischer Daten entsteht. Der DeepBlue Epigenomic Data Server und sein Ökosystem wurden vom International Human Epigenome Consortium äußerst gut aufgenommen und erreichten seit ihrer Veröffentlichung große Aufmerksamkeit bei der epigenomischen Forschungsgemeinschaft mit derzeit 160 registrierten Benutzern und mehr als drei Millionen anonymen Verarbeitungsanforderungen

POTENTIAL SELECTIVITY OF HERBICIDES IN PRE- AND POST-EMERGENT LINSEED (LINUM USITATISSIMUM L.)

A linhaça é uma oleaginosa amplamente utilizada na alimentação humana e animal, como cultura de cobertura em agroecossistemas e para produção de fibras. Para facilitar o manejo de plantas daninhas na cultura, este trabalho teve como objetivo avaliar potenciais herbicidas seletivos para o cultivo de linhaça aplicados em pré-plantio incorporado (PPI), pré-emergência (PRE), pós-emergência inicial (POS), pós-emergência tardia (POS tardio) uma vez que ainda não existem herbicidas registrados para uso em linhaça no Brasil. Portanto, quatro experimentos foram conduzidos em delineamento inteiramente casualizado com quatro repetições, e cinco (exp. 1), 21 (exp. 2), 26 (exp. 3) e quatro (exp. 4) tratamentos. Foram avaliadas a injúria na cultura e a matéria fresca e seca das plantas. O Experimento 4 foi conduzido até a produção de sementes, obtendo-se os dados de altura final, número de cápsulas e produtividade. Os resultados foram caracterizados pela baixa seletividade dos herbicidas durante a pré-emergência, incorporados ou não, e indicaram 11 herbicidas com potencial seletividade na pós-emergência, seja precoce ou tardia, os quais foram: bentazon, bentazon + imazamox, clethodim + fenoxaprop, clethodim, flumiclorac, fluazifop, flumioxazin, haloxyfop, nicosulfuron, tembotrione e tepraloxydim. A linhaça demonstrou ser suscetível ou com baixa tolerância a vários herbicidas.Linseed is an oilseed crop that is widely used in human and animal feed, as a cover crop in agroecosystems, and for fiber production. To facilitate the management of weeds in the crop, this study aimed to evaluate potential selective herbicides for linseed cultivation applied in pre-planting and incorporation (PPI), pre-emergence (PRE), and early (POST) and late (late POST) post-emergence stages, since there are presently no herbicides registered for use on linseed in Brazil. Therefore, four experiments were conducted in a completely randomized design with four replications, and five (exp. 1), 21 (exp. 2), 26 (exp. 3), and four (exp. 4) treatments. Crop injury and the fresh and dry matter of the plants were evaluated. Experiment 4 was conducted until seed production, and data on the final height, number of capsules, and yield were obtained. The results were characterized by the low selectivity of herbicides during pre-emergence, whether incorporated or not, and indicated 11 herbicides with potential selectivity in post-emergence, whether early or late, namely: bentazon, bentazon + imazamox, clethodim + fenoxaprop, clethodim, flumiclorac, fluazifop, flumioxazin, haloxyfop, nicosulfuron, tembotrione, and tepraloxydim. Linseed is demonstrated to be susceptible to or has low tolerance to various herbicides

Eficácia de herbicidas aplicados em trapoeraba (Commelina benghalensis) na região oeste do Estado do Paraná

Ragweed (Commelina spp.) is considered a genus tolerant to glyphosate, with reduced control of this herbicide in advanced stages. Thus, the aim of this study was to evaluate the effectiveness of controlling associations of glyphosate with herbicides with different mechanisms of action in Commelina benghalensis. The experiment was carried out, after the harvest of the off-season corn in 2018, in Palotina-PR. The experimental design was randomized blocks with 12 treatments (Control, glyphosate + 2,4-D, glyphosate + 2,4-D (aminol 806), glyphosate + dicamba, saflufenacil + glyphosate, glyphosate + dicamba + saflufenacil, diclosulam + glyphosate + saflufenacil, glyphosate + dicamba + chlorimuron, glyphosate + dicamba + glufosinate, glyphosate + dicamba + diclosula, glyphosate + dicamba + (sulfentrazone + diuron) and glyphosate + dicamba + (imazethapyr + flumioxazin) and 4 replicates. 7, 14, 21 and 28 days after application (DAA) and through dry mass at 28 DAA. Regardless of the treatment, at 7 DAA there was no effective control. The scores increased over time, and at 28 DAA, treatments glyphosate + 2,4-D for both doses (1025+975 and 1080+1005); diclosulam + glyphosate + saflufenacil; glyphosate + dicamba + diclosulam and glyphosate + dicamba + (imazethapyr + flumioxazin) were the most effective in the control and reduction of dry mass, reducing the possible associations in the control of ragweed.A trapoeraba (Commelina spp.) é considerada um gênero tolerante ao glyphosate, apresentando controle reduzido a esse herbicida em estádios avançados. Assim, o objetivo do trabalho foi avaliar a eficácia de controle das associações de glyphosate com herbicidas de diferentes mecanismos de ação em Commelina benghalensis. O experimento foi conduzido, após a colheita do milho safrinha em 2018, em Palotina-PR. O delineamento experimental foi de blocos casualizados com 12 tratamentos (Testemunha, glyphosate + 2,4-D, glyphosate + 2,4-D (aminol 806), glyphosate + dicamba, saflufenacil + glyphosate, glyphosate + dicamba + saflufenacil, diclosulam + glyphosate + saflufenacil, glyphosate + dicamba + chlorimuron, glyphosate + dicamba + glufosinato, glyphosate + dicamba + diclosula, glyphosate + dicamba + (sulfentrazona + diuron) e glyphosate + dicamba + (imazetapir + flumioxazina) e 4 repetições. O controle de C. benghalensis foi avaliado por notas visuais aos 7, 14, 21 e 28 dias após a aplicação (DAA) e por meio da massa seca aos 28 DAA. Independente do tratamento, aos 7 DAA não houve controle eficaz. As notas foram crescentes ao longo do tempo, sendo que aos 28 DAA, os tratamentos glyphosate + 2,4-D para ambas as doses (1025+975 e 1080+1005); diclosulam + glyphosate + saflufenacil; glyphosate + dicamba + diclosulam e glyphosate + dicamba + (imazetapir + flumioxazina) foram os mais eficazes no controle e redução de massa seca, indicando ser potenciais associações no controle da trapoeraba

Alternativas ao paraquat para o controle químico de azevém, aveia e buva

With the banning of paraquat, it is necessary to plan for the use of alternative herbicides in the desiccation of weeds. In this sense, herbicides such as glufosinate, saflufenacil, diquat, glyphosate, clethodim are highlighted in different mixtures. Glufosinate, especially in mixtures, is believed to be effective in controlling Lolium perenne ssp. multiflorum (Italian ryegrass), Avena fatua (wild oat) and/or Conyza sumatrensis (Sumatran fleabane). The aim was to evaluate the efficacy of glufosinate alone, or in mixtures, in the control of Italian ryegrass, wild oat and Sumatran fleabane, as an alternative to paraquat. The experiment was carried out in an experimental area located in the city of Cruz Alta, state of Rio Grande do Sul (RS), Brazil, in November 2020. A completely randomized design was used, with four replications. The treatments consisted of the application of glufosinate, saflufenacil, diquat, glyphosate and clethodim, alone or in combinations. The control of Italian ryegrass, wild oat and Sumatran fleabane was evaluated at 7, 14, and 28 days after application. Glufosinate at mixtures was effective in controlling weeds, being almost always superior to that observed for diquat alone or in mixtures. To achieve the same efficacy of the mixtures, the rate of glufosinate must be at least 700 g a.i. ha-1. The application of glufosinate (400 g a.i. ha-1) in mixtures with saflufenacil, glyphosate and clethodim was effective in controlling Italian ryegrass, wild oat and Sumatran fleabane. The alone application of glufosinate proved to be effective in controlling all weeds at the maximum applied dose (700 g a.i. ha-1). Glufosinate, alone or in mixtures, is thus characterized as an alternative to paraquat in the control of weeds.Com o banimento do paraquat, é necessário planejar o uso de herbicidas alternativos na dessecação de plantas daninhas. Neste sentido desatacam-se herbicidas como glufosinate, saflufenacil, diquat, glyphosate, clethodim, em diferentes associações. Acredita-se que o glufosinate, sobretudo em associações, seja eficaz no controle de Lolium perenne ssp. multiflorum (azevém), Avena fatua (aveia) e/ou Conyza sumatrensis (buva). Objetivou-se avaliar a eficácia de glufosinate isolado, ou em associações, no controle de azevém, aveia e buva, como alternativa ao paraquat. O experimento foi conduzido em área experimental  localizada no município de Cruz Alta, estado do Rio Grande do Sul (RS), Brasil, em novembro de 2020. Foi utilizado delineamento inteiramente casualizado, com quatro repetições. Os tratamentos foram compostos pela aplicação de glufosinate, saflufenacil, diquat, glyphosate e clethodim, isolados ou em associações. Foi avaliado o controle de azevém, aveia e buva, aos 7, 14 e 28 dias após aplicação. O glufosinate em associações foi eficaz no controle das plantas daninhas, sendo quase sempre superior ao observado para diquat isolado ou em misturas. Para se antingir a mesma eficácia das associações, a dose de glufosinate deve ser de no mínimo 700 g i.a. ha-1. A aplicação de glufosinate (400 g i.a. ha-1) em associações com saflufenacil, glyphosate e clethodim foi eficaz no controle de azevém, aveia e buva. A aplicação isolada de glufosinate se mostrou eficaz no controle de todas as plantas daninhas na dose máxima aplicada (700 g i.a. ha-1). O glufosinate, isolado ou em associações, caracteriza-se assim alternativa ao paraquat no controle de plantas daninhas

A Gibbs approach to Chargaff's second parity rule

Chargaff's second parity rule (CSPR) asserts that the frequencies of short polynucleotide chains are the same as those of the complementary reversed chains. Up to now, this hypothesis has only been observed empirically and there is currently no explanation for its presence in DNA strands. Here we argue that CSPR is a probabilistic consequence of the reverse complementarity between paired strands, because the Gibbs distribution associated with the chemical energy between the bonds satisfies CSPR. We develop a statistical test to study the validity of CSPR under the Gibbsian assumption and we apply it to a large set of bacterial genomes taken from the GenBank repository.Comment: 16 page

Sequential application of herbicide options for controlling Conyza sumatrensis in soybean pre-sowing

The aim of this study was to evaluate the efficacy of sequentially applied herbicides to control Conyza sumatrensis, one of the most widely distributed weeds worldwide, in soybean pre-sowing burndown. The study was conducted under field conditions in the state of Paraná, Brazil, at 2018-2019 growing season. The experiment consisted of a randomized block design with four replicates, with 12 treatments consisting of different herbicide mixtures applied before sowing. Control of C. sumatrensis, injury to soybean plants, and variables related to agronomic performance were evaluated. The control levels were high for all treatments, except for the one that was free of saflufenacil in either of the two applications. These results highlight the importance of saflufenacil in the control of C. sumatrensis and show promise for the use of saflufenacil/imazethapyr when considering the system and other weeds. All studied treatments were selective to soybean, which showed higher injury values in the presence of diclosulam; however, this did not compromise the agronomic performance of soybean. Highlights • Application of systemic herbicides with sequential application of burndown herbicides, is essential for the control of Conyza sumatrensis (>15 cm height).• Saflufenacil, flumioxazin, and imazethapyr stand out in the control of Conyza sumatrensis.• Protox and ALS inhibitors can replace paraquat in sequential application with equal efficacy in the control of Conyza sumatrensis.The aim of this study was to evaluate the efficacy of sequentially applied herbicides to control Conyza sumatrensis, one of the most widely distributed weeds worldwide, in soybean pre-sowing burndown. The study was conducted under field conditions in the state of Paraná, Brazil, at 2018-2019 growing season. The experiment consisted of a randomized block design with four replicates, with 12 treatments consisting of different herbicide mixtures applied before sowing. Control of C. sumatrensis, injury to soybean plants, and variables related to agronomic performance were evaluated. The control levels were high for all treatments, except for the one that was free of saflufenacil in either of the two applications. These results highlight the importance of saflufenacil in the control of C. sumatrensis and show promise for the use of saflufenacil/imazethapyr when considering the system and other weeds. All studied treatments were selective to soybean, which showed higher injury values in the presence of diclosulam; however, this did not compromise the agronomic performance of soybean. Highlights • Application of systemic herbicides with sequential application of burndown herbicides, is essential for the control of Conyza sumatrensis (>15 cm height).• Saflufenacil, flumioxazin, and imazethapyr stand out in the control of Conyza sumatrensis.• Protox and ALS inhibitors can replace paraquat in sequential application with equal efficacy in the control of Conyza sumatrensis

Mixtures between glyphosate formulations and ACCase-inhibiting herbicides in the control of Chloris elata

Chloris elata is an important weed for grain and sugarcane crops. In addition to its aggressiveness, it may show resistance to glyphosate herbicide. In this context, the aim of this study was to assess the effectiveness of glyphosate formulations, isolated or in association with ACCase inhibitors, in controlling C. elata (putatively resistant to glyphosate) at different developmental stages. Four experiments were conducted in a completely randomized design. Treatments consisted of glyphosate application under different formulations with ACCase inhibitors, isolated or in mixtures. Applications were carried out at the stages of four fully expanded leaves in Experiment I, four tillers in Experiment II, and at regrowth of the four-tiller plants in Experiments III and IV. Applications of glyphosate isopropylamine salt associated with sethoxydim or clethodim showed to be among the best treatments in Experiments I, II, and III, presenting control scores equal to or greater than 90%. However, not even these treatments could provide successful control in Experiment IV. Moreover, and regardless of the formulation, isolated glyphosate, showed 85% (Experiment III) and 50% (Experiment IV) maximum controls. Associations between glyphosate and ACCase-inhibiting herbicides showed to be effective in controlling C. elata, especially at early developmental stages. In general, isolated herbicides provided lower percentages of control, as well as higher values of dry matter. Sole herbicide applications were not effective in controlling C. elata (putatively resistant to glyphosate), regardless of the developmental stage. Highlights: Mixtures between glyphosate and ACCase-inhibiting have been shown to be effective in C. elata control, especially in the early development stages. Isolated herbicide applications were not effective in controlling C. elata, regardless of the development stage. Mixtures between glyphosate and ACCase-inhibiting is more important in the control than the glyphosate formulation or ACCase-inhibiting used.Chloris elata is an important weed for grain and sugarcane crops. In addition to its aggressiveness, it may show resistance to glyphosate herbicide. In this context, the aim of this study was to assess the effectiveness of glyphosate formulations, isolated or in association with ACCase inhibitors, in controlling C. elata (putatively resistant to glyphosate) at different developmental stages. Four experiments were conducted in a completely randomized design. Treatments consisted of glyphosate application under different formulations with ACCase inhibitors, isolated or in mixtures. Applications were carried out at the stages of four fully expanded leaves in Experiment I, four tillers in Experiment II, and at regrowth of the four-tiller plants in Experiments III and IV. Applications of glyphosate isopropylamine salt associated with sethoxydim or clethodim showed to be among the best treatments in Experiments I, II, and III, presenting control scores equal to or greater than 90%. However, not even these treatments could provide successful control in Experiment IV. Moreover, and regardless of the formulation, isolated glyphosate, showed 85% (Experiment III) and 50% (Experiment IV) maximum controls. Associations between glyphosate and ACCase-inhibiting herbicides showed to be effective in controlling C. elata, especially at early developmental stages. In general, isolated herbicides provided lower percentages of control, as well as higher values of dry matter. Sole herbicide applications were not effective in controlling C. elata (putatively resistant to glyphosate), regardless of the developmental stage. Highlights: Mixtures between glyphosate and ACCase-inhibiting have been shown to be effective in C. elata control, especially in the early development stages. Isolated herbicide applications were not effective in controlling C. elata, regardless of the development stage. Mixtures between glyphosate and ACCase-inhibiting is more important in the control than the glyphosate formulation or ACCase-inhibiting used

Democracia y tecnologías de la información y de la comunicación: hacia un marco de referencia para inhibir el fraude en los procesos electorales mediante el uso de TIC

Historically, electoral processes have been susceptible to fraud. The electoral laws in different countries try, in a greater or lesser extent, to protect the electoral processes from fraudulent actions through procedures and technological mechanisms. In the electoral process, the implementation of information and communication technologies has played an important role and, as a result, in some countries, the level of fraud has been reduced. In this paper, we identify the factors that influence the conduct of electoral fraud, based on the classical theory of the fraud triangle. The focus of the paper is to identify perceived opportunities (one of the elements of the fraud triangle). In the paper, the electoral process is conceptualized and an example, using the model, is presented. Based on this conceptual model, a framework is proposed to help identify the perceived opportunities to commit fraud.Los procesos electorales, históricamente, han sido susceptibles de fraude. Las legislaciones electorales de los países tratan, en mayor o menor grado, de proteger los procesos electorales de acciones fraudulentas, a través de procedimientos e incluso de mecanismos tecnológicos. En algunos casos, la implementación de tecnologías de la información y de la comunicación ha jugado un papel importante en ese sentido y, en algunos países, se ha logrado disminuir el nivel de fraude. En este trabajo se propone identificar los factores que influyen en el cometimiento de un fraude electoral, a partir de la teoría clásica del triángulo del fraude. El enfoque principal es identificar las oportunidades percibidas (uno de los elementos del triángulo del fraude). Se conceptualiza el proceso electoral y se presenta el modelo de una instancia particular. A partir de ese modelo conceptual se propone un marco de referencia que ayudará a identificar las oportunidades percibidas de cometer fraude