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RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper ( Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “ Salsa ”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.

The study of biocultural diversity requires the use of appropriate concepts and analytical tools. Particularly, there is a need of indices capable to show the degree of stratification in the set of interactions among cultures and groups of plants and animals in a given region. Here, we present a mathematical approach based on the mutual Shannon information theory to study the relationships among cultural and biological groups. Biocultural complexity was described in terms of effective biocultural units, a new concept defined in this work. From the mathematical formulation of biocultural complexity, formulas were derived to measure the specificity of biological groups and the specialization of cultures, based on the association of human societies with plant or animal groups. To exemplify the concepts and tools, two data sets were analyzed; 1) a set that included artificial data in order to demonstrate the use of the formulas and calculate the indices, and 2) a set that included published data on the use of 18 mushroom species by people in five villages of eastern India. Analysis of the first data set revealed a clear case of biocultural complexity, whereas that of the second set showed that the villages and the use of biological resources composed a single biocultural unit. Overall, hypothesis testing of the association among cultures and biological species was consistent with the information that was provided by the new indices.

Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell components and thus define the 'minimal cell' and the corresponding 'minimal genome', we postulate that the synthesis of all cell elements can be represented as a finite set of binary operators, and within this framework we show that cell elements that depend on their previous existence to be synthesized are those that are essential for cell survival. An algorithm to distinguish essential cell elements is presented and demonstrated within an interactome. Data and functions implementing the algorithm are given as supporting information. We expect that this algorithmic approach will lead to the determination of the complete interactome of the minimal cell, which could then be experimentally validated. The assumptions behind this hypothesis as well as its consequences for experimental and theoretical biology are discussed.

The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. In any case, it is difficult to completely comprehend the global changes that occur in the transcriptome, given that thousands of gene expression measurements are involved. We propose an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. We define transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either housekeeping or highly specific genes and clarifying the meaning of these concepts in the literature. Tissue specialization is measured by average gene specificity. We introduce the formulae using a simple example and show their application in two datasets of gene expression in human tissues. Visualization of the positions of transcriptomes in a system of diversity and specialization coordinates makes it possible to understand at a glance their interrelations, summarizing in a powerful way which transcriptomes are richer in diversity of expressed genes, or which are relatively more specialized. The framework presented enlightens the relation among transcriptomes, allowing a better understanding of their changes through the development of the organism or in response to environmental stimuli.

Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation of gene expression. The purpose of this study was to estimate the changes in transcriptome diversity and specialization, as well as gene specificities during fruit development in this crop, and to illustrate the advantages of estimating these parameters. To achieve these aims, we programmed and made publicly available an R package. In this study, we applied these methods to a set of 179 RNA-Seq libraries from a factorial experiment that includes 12 different genotypes at various stages of fruit development. We found that the diversity of the transcriptome decreases linearly from the flower to the mature fruit, while its specialization follows a complex and non-linear behavior during this process. Additionally, by defining sets of genes with different degrees of specialization and applying Gene Ontology enrichment analysis, we identified processes, functions, and components that play a central role in particular fruit development stages. In conclusion, the estimation of diversity, specialization, and specificity summarizes the global properties of the transcriptomes, providing insights that are difficult to achieve by other means.

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

Cotton (genus Gossypium ) is an important agricultural crop around the world because of its fiber. Gossypium turneri Fryxell is a wild cotton species endemic to the state of Sonora (northwestern Mexico), whose status has been recently raised to endangered in the IUCN Red List. This species has invaluable characteristics that could be useful in the cultivated cotton gene pool. Despite its importance, G. turneri has been studied very little. To the best of our knowledge, no previous study has characterized its seed morphology and cytogenetics. Therefore, in the present study the seed morphology and karyotype of G. turneri were analyzed. Seeds of G. turneri have nonuniform oval shape and brown-gray color. This species produces short fibers attached to its seed surface that are not long enough for commercial use. Our seed sizes were greater than those previously described for G. turneri and other diploid cottons. The length and width of seeds were 8.80 mm and 4.83 mm, respectively. Traits such as embryo and seed coat were measured and carefully observed, and gossypol glands were observed only in the embryo during the evaluation of internal features of seeds. Cytogenetic analysis revealed 26 chromosomes (2n = 2x = 26) in mitotic cells of G. turneri . The karyotype analysis showed mainly metacentric (m), submetacentric (sm) and subtelocentric (st) chromosomes. Our results reveal important biological traits of G. turneri that could be considered in future studies to improve cultivated cotton.

The objective of the present work was to study the soil solution throughout time in pots under greenhouse conditions. The work consisted of monitoring the solution of calcareous soil and forest soil in the absence of plants, with different types of fertilization: treatment 1: absolute control (irrigation water); treatment 2: Steiner nutrient solution; treatment 3: solid fertilizers; and treatment 4: vermicompost tea (aqueous extract). The samples were collected weekly using lysimeters for 14 weeks. They were analyzed to determine the nitrate content, total nitrogen, calcium, potassium, magnesium, sodium, sulfur, zinc, boron, pH, electrical conductivity, and oxide-reduction potential. To understand the interactions between treatments, soil type, and time over ion behavior and availability, linear and polynomial models were used, selected by a cross-validation method, which resulted in robust models, where it was found that the pH behavior is associated with the type of fertilization and soil type, with the elapsed time being a nonsignificant factor. On the other hand, time influenced the dynamics of the remaining ions and their availability. It was found that the multiple polynomial model fit better for the variables: potassium, calcium, sodium (square degree), electrical conductivity, nitrates, sulfur (cubic degree), zinc, oxidation-reduction potential, nitrogen, magnesium, and boron (quartic degree).

Plants from arid zones of Mexico are an interesting source of phytochemicals that exhibit a large number of biological properties. In this context, Rhus microphylla (Rm) and Myrtillocactus geometrizans (Mg) fruits have been used as folk remedies and to make traditional foods, respectively; however, studies on their composition and bioactivity are limited. Thus, the objective of this work was to evaluate the yields, phenolic composition, and bioactive properties (scavenging and reducing capacities, antiproliferative, and antifungal) of aqueous and hydroalcohol extracts of Rm and Mg fruits obtained by conventional agitation and ohmic heating (OH). The results showed that the Rm fruit extracts had the highest total phenolic content (TPC) values and the strongest scavenging and reducing capacities compared to those of Mg fruits, being characterized by the presence of gallic acid, while the composition of the Mg extracts varied with respect to the extraction conditions used. Regarding antifungal activity in vitro against two phytopathogenic fungi, Rhizopus stolonifer and Fusarium oxysporum, the hydroalcohol extracts obtained by conventional agitation of both plants (RmH-C and MgH-C) showed the best inhibitory effect, respectively. Interestingly, none of the extracts under study presented cytotoxicity against the noncancerous ARPE-19 cell line, while three extracts of Rm fruit exhibited a moderate antiproliferative activity against HeLa (cancerous) cell line. These findings reveal for the first time the potential of Rm and Mg fruits as a new source of bioactive compounds for future industrial applications.

The presence and levels of transgenic maize in Mexico and the effect this could have on local landraces or closely related species such as teosinte has been the subject of several previous reports, some showing contrasting results. Cultural, social and political factors all affect maize cultivation in Mexico and although since 1998 there has been a moratorium on the commercial cultivation of transgenic maize, Mexico imports maize, mainly from the USA where transgenic cultivars are widely grown. Additionally extensive migration between rural areas in Mexico and the USA and customs of seed exchange between farmers may also play an unintentional role in the establishment of transgenic seed. A comprehensive study of all Mexican maize landraces throughout the country is not feasible, however this report presents data based on analysis of 3204 maize accessions obtained from the central region of Mexico (where permits have never been authorized for cultivation of transgenic maize) and the northern region (where for a short period authorization for experimental plots was granted). The results of the study confirm that transgenes are present in all the geographical areas sampled and were more common in germplasm obtained in the northern region. However, there was no evidence that regions where field trials had been authorized showed higher levels of transgene presence or that the morphology of seed lots harboring transgenic material was significantly modified in favor of expected transgenic phenotypes.