Cancer Reduces Transcriptome Specialization

A central goal of cancer biology is to understand how cells from this family of genetic diseases undergo specific morphological and physiological changes and regress to a de-regulated state of the cell cycle. The fact that tumors are unable to perform most of the specific functions of the original tissue led us to hypothesize that the degree of specialization of the transcriptome of cancerous tissues must be less than their normal counterparts. With the aid of information theory tools, we analyzed four datasets derived from transcriptomes of normal and tumor tissues to quantitatively test the hypothesis that cancer reduces transcriptome specialization. Here, we show that the transcriptional specialization of a tumor is significantly less than the corresponding normal tissue and comparable with the specialization of dedifferentiated embryonic stem cells. Furthermore, we demonstrate that the drop in specialization in cancerous tissues is largely due to a decrease in expression of genes that are highly specific to the normal organ. This approach gives us a better understanding of carcinogenesis and offers new tools for the identification of genes that are highly influential in cancer progression

Obtención de híbridos intergenéricos Helianthus annuus x Tithonia rotundifolia y su análisis morfológico y molecular

Hybridization between the cultivated sunflower Helianthus annuus and the wild species with ornamental potential Tithonia rotundifolia was performed. From three cultivated materials: AN-3, Primavera and HA 89, the only success was obtained with the public cultivated sunflower line HA 89 as female parent. The male parent was a T. rotundifolia population collected in the state of Guerrero, Mexico. A total of 826 well developed hybrid achenes were produced, with a rate of success of four in 1000 potential achenes. In a sample of 49 plants established in the experimental field, two phenotypic classes were observed: a) plants with many small inflorescenses, and b) plants with a single big head and a few or none axillary inflorescenses. Both types were morphologically characterized and showed a clearly hybrid morphology. Additionally, the AFLP-based DNA fingerprints were analyzed in a sample of ten familial trios, with an average of 28 polymorphisms per trio. The DNA fingerprinting analysis of the plants complemented the morphological study, allowed confirmation of the hybrid nature of the progenies and ruled out the partial hybridization phenomenon. All the hybrid plants showed sterility. From this work, it becomes clear that chromosomic manipulation or tissue culture techniques are needed to develop fertile hybrids with ornamental potential.Se realizó el cruzamiento entre el girasol cultivado Helianthus annuus y la especie silvestre con potencial ornamental Tithonia rotundifolia. De tres materiales cultivados: AN-3, Primavera y HA 89, sólo se tuvo éxito con la línea pública de girasol cultivado HA 89 como progenitor femenino. A su vez el masculino fue una población de T. rotundifolia recolectada en el estado de Guerrero, México. Se produjeron 826 aquenios híbridos bien desarrollados, con una tasa de éxito de cuatro en 1000 aquenios potenciales. Dentro de una muestra de 49 plantas establecidas en el campo experimental, se observaron dos clases fenotípicas: a) individuos con muchas inflorescencias pequeñas y b) otros con cabezuela solitaria grande y con pocas o ninguna inflorescencia axilar. Ambos tipos fueron caracterizados morfológicamente y presentaron rasgos claramente híbridos. Además, se analizó la huella genética, a través del polimorfismo en la longitud de los fragmentos amplificados (AFLPs), de una muestra de diez tríos familiares de cruzamientos, con un promedio de 28 polimorfismos por trío. El análisis de huella genética de las plantas complementó al estudio morfológico, permitió constatar la naturaleza híbrida de las progenies y descartar el fenómeno del cruzamiento parcial. Todas las plantas experimentales obtenidas resultaron ser estériles. Del presente trabajo se desprende que se requiere de manipulación cromosómica o técnicas de cultivo de tejidos para el desarrollo de híbridos fértiles con potencial ornamental

Rescate de embriones en híbridos intergenéricos Helianthus annuus x Tithonia rotundifolia

In this research an in vitro technique was developed for production and propagation of intergeneric hybrids from immature seeds produced by crossing the domestic sunflower Helianthus annuus and the wild species Tithonia rotundifolia (Mill.) S. F. Blake. For embryo rescue in tissue culture the greatest success was obtained with the sequential use of three Murashige-Skoog based media: a) with amino acids and growth regulator BAP for germination, b) without amino acids and with BAP for micropropagation, and c) without vitamins and growth regulator ANA for root development. The amino acids were added as a source of organic nitrogen. From a single seedling a total of 130 healthy plantlets were obtained. Twenty of them were taken for acclimatization, and only one reached an incomplete flowering stage. Therefore, standardizing acclimatization conditions is still required. In particular, it is necessary to establish treatments that allow a clear definition of the specific conditions for the acclimatization of the hybrid, through the test of different substrate mixtures and nutritive solutions under controlled environmental conditions. It is recommended to try the use of retardants and amino acids, as well as modifications in light intensity.En esta investigación se desarrolló una técnica in vitro para producir y propagar híbridos intergenéricos a partir de semillas inmaduras producto del cruzamiento del girasol cultivado Helianthus annuus L. con la especie silvestre Tithonia rotundifolia (Mill.) S. F. Blake. Para el rescate de embriones inmaduros en cultivo de tejidos el mayor éxito se obtuvo con el uso secuencial de tres medios basados en el de Murashige-Skoog: a) con adición de aminoácidos y el regulador de crecimiento BAP para germinación, b) sin aminoácidos y con BAP para micropropagación, y c) sin vitaminas y con el regulador de crecimiento ANA para enraizamiento. Los aminoácidos se agregaron como fuente de nitrógeno orgánico. A partir de una plántula se lograron obtener 130 en buenas condiciones de sanidad. Veinte de ellas se llevaron a aclimatación, y solamente una generó botones y llegó a floración inconclusa, por lo que aún se requiere estandarizar las condiciones de aclimatación. En particular, se necesita establecer tratamientos que permitan definir con claridad las condiciones específicas para aclimatar el híbrido, a través de la prueba de diferentes mezclas de sustratos y soluciones nutritivas bajo condiciones ambientales controladas. Se recomienda probar el manejo de retardantes y aminoácidos, así como realizar modificaciones en la intensidad de luz

Worldwide selection footprints for drought and heat in bread wheat (Triticum aestivum L.)

Genome–environment Associations (GEA) or Environmental Genome-Wide Association scans (EnvGWAS) have been poorly applied for studying the genomics of adaptive traits in bread wheat landraces (Triticum aestivum L.). We analyzed 990 landraces and seven climatic variables (mean temperature, maximum temperature, precipitation, precipitation seasonality, heat index of mean temperature, heat index of maximum temperature, and drought index) in GEA using the FarmCPU approach with GAPIT. Historical temperature and precipitation values were obtained as monthly averages from 1970 to 2000. Based on 26,064 high-quality SNP loci, landraces were classified into ten subpopulations exhibiting high genetic differentiation. The GEA identified 59 SNPs and nearly 89 protein-encoding genes involved in the response processes to abiotic stress. Genes related to biosynthesis and signaling are mainly mediated by auxins, abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonates (JA), which are known to operate together in modulation responses to heat stress and drought in plants. In addition, we identified some proteins associated with the response and tolerance to stress by high temperatures, water deficit, and cell wall functions. The results provide candidate regions for selection aimed to improve drought and heat tolerance in bread wheat and provide insights into the genetic mechanisms involved in adaptation to extreme environments

Asociación entre la composición elemental del suelo y la planta y la morfología de <em>Dasylirion cedrosanum</em> Trel.

Antecedentes: La producción de sotol ha crecido en los últimos años. Existe el interés de establecer monocultivos para mitigar la sobreexplotación de las poblaciones silvestres. Sin embargo, para un establecimiento y manejo eficiente de plantaciones es importante conocer la composición elemental de Dasylirion cedrosanum. Hipótesis: La composición mineral de Dasylirion cedrosanum refleja la composición mineral de la solución del suelo del sitio en donde crece. Especie de estudio: Dasylirion cedrosanum Trel. Sitios y años de estudio: Se muestrearon plantas y suelos durante septiembre y octubre del 2020 en San Lorenzo, Buenavista y General Cepeda, Coahuila. Métodos: Se colectaron tallos, hojas y suelos y se analizaron sus elementos. Además, se midieron caracteres morfológicos a cada espécimen. Los datos se analizaron con técnicas estadísticas multivariadas. Resultados: El Ca y N presentaron alta concentración en el suelo y en las plantas. En las tres localidades los niveles de Se fueron altos en las plantas. No obstante, el Se en la solución del suelo no fue detectable. Los individuos de San Lorenzo y General Cepeda mostraron niveles altos de Cu y Ba, a pesar de que el Cu no fue detectable en el suelo. El crecimiento mostró asociación negativa con el As, Ba, Cd, Cr, Mo, Ni y Pb y el Mg estuvo relacionado con un mayor crecimiento de Dasylirion cedrosanum. Conclusiones: Dasylirion cedrosanum dispone de mecanismos para la adquisición y concentración de los elementos de la solución del suelo, incluso cuando estos estén en concentraciones bajas

Development of tomatillo (Physalis ixocarpa Brot.) autotetraploids and their chromosome and phenotypic characterization

The tomatillo, Physalis ixocarpa Brot. (2n = 2x = 24), is an important crop in Mexico, and it is becoming appreciated in other countries. Polyploidy induction is expected to increase its breeding potential. The objective of this work was to develop and characterize tomatillo autotetraploids through colchicine-based induction. Young seedlings of the Rendidora cultivar were treated for 24 h with colchicine in concentrations ranging from 0.04% to 0.20%, and ploidy levels were tested by cytological and flow cytometry techniques. Autotetraploidy was induced with colchicine concentrations of 0.12% and 0.16%, with success rates of 67% and 65%, respectively. Presence of univalents, bivalents and multivalents was observed in prophase I and metaphase I. The basic genome size was not altered in the third generation progeny from treated plants. Autotetraploid plants were fertile and productive, but their pollen development was lower than their diploid counterpart. The polyploid plants showed higher values for life cycle length, plant height, fruit weight and equatorial diameter, fruits per plant, and soluble solid concentration. This is the first report of an autopolyploid cultivated tomatillo. Its genome duplication is readily induced with production of fertile plants, and may be valuable to introduce genetic plasticity in this crop

Transcriptome analyses throughout chili pepper fruit development reveal novel insights into the domestication process

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

On an algorithmic definition for the components of the minimal cell.

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