The Critical Point of Conventionally Bred Soft Wheat Varieties in Organic Farming Systems

Nowdays, wheat is the most important crop for organic farming system. However, the varieties breeded and tested in the conditions of organic farming system are still missing. It gives rise to very low level of yield in the Czech Republic (less than 50% of level of convention one in the same conditions). One of the reasons is that the ideotype of organic breeded variety is different from conventional one. The varieties suitable for organic farming system differ in many respects from those adopted in conventional farming. The first difference is obvious from the conventional tests of use value of the varieties, taking just some direct indicators influencing the main parameter (yield) into account. Generally speaking, the features to be tested can be divided into 4 groups: the morphological, the biological, the economic and quality parameters. The conventional varieties are bred in conditions characterised by an abundance of soluble nutrients, and therefore, their root systems are not adapted to an insufficiency of nutrients or weaker bonding of nutrients. The competitiveness to weeds has also been ignored. Any conventional variety, which has never confronted any strong weeds during the breeding process, cannot be assumed to be competitive enough in the conditions of an organic agroecosystem. Resistance to diseases and pests can be similarly characterised. The variety is protected by pesticides throughout the conventional breeding process. Because of the seasonal fluctuations in weather, we need a plastic and flexible variety. They are also different from the point of view of their qualitative parameters

Wheat Growing and Quality in Organic Farming

This chapter will present criteria of the selection of suitable varieties for the organic farming system, depending on land and climatic conditions of a farm, current legislation, availability of seeds, options of the final use, etc. Data in this chapter are based on results of the trials carried out by authors on their working places and a discussion on o given topic. Exact small-plot trials with particular selected varieties (bread and hard wheat) and genetic resources of hulled wheat species (einkorn, emmer wheat, spelt wheat) were established on the authors' working places between 2005 and 2010. Significant and important characteristics for the organic farming (morphological, biological characteristics, yield formation and structure of yield, qualitative parametres of the production)

Histone H4 acetylation regulates behavioral inter-individual variability in zebrafish

FUNDAMENTOS: Los animales pueden mostrar comportamientos muy diferentes incluso en poblaciones isogénicas, pero los mecanismos subyacentes para generar esta variabilidad siguen siendo esquivos. Utilizamos el pez cebra (Danio rerio) como modelo para probar la influencia de las modificaciones de las histonas en el comportamiento. RESULTADOS: Encontramos que las larvas de pez cebra de laboratorio e isogénico muestran comportamientos individuales consistentes cuando nadan libremente en pozos idénticos o en reacción a estímulos. Esta variabilidad de comportamiento interindividual se reduce cuando dañamos la vía de desacetilación de la histona. Los individuos con altos niveles de acetilación de la histona H4, y específicamente H4K12, se comportan de manera similar al promedio de la población, pero aquellos con bajos niveles se desvían de él. Más precisamente, encontramos un conjunto de regiones genómicas cuya acetilación de histonas H4 se reduce con la distancia entre el individuo y el comportamiento medio de la población. Encontramos pruebas de que esta modulación depende de un complejo de Yin-yang 1 (YY1) y de la histona deacetilasa 1 (HDAC1) que se une a estas regiones y las desactiva. Estos cambios no sólo se mantienen a nivel de la transcripción sino que también se amplifican, ya que la mayoría de las regiones objetivo se encuentran cerca de los genes que codifican los factores de transcripción. CONCLUSIONES: Sugerimos que la estocasticidad en la vía de desacetilación de las histonas participa en la generación de una variabilidad interindividual de comportamiento genético independiente.BACKGROUND: Animals can show very different behaviors even in isogenic populations, but the underlying mechanisms to generate this variability remain elusive. We use the zebrafish (Danio rerio) as a model to test the influence of histone modifications on behavior. RESULTS: We find that laboratory and isogenic zebrafish larvae show consistent individual behaviors when swimming freely in identical wells or in reaction to stimuli. This behavioral inter-individual variability is reduced when we impair the histone deacetylation pathway. Individuals with high levels of histone H4 acetylation, and specifically H4K12, behave similarly to the average of the population, but those with low levels deviate from it. More precisely, we find a set of genomic regions whose histone H4 acetylation is reduced with the distance between the individual and the average population behavior. We find evidence that this modulation depends on a complex of Yin-yang 1 (YY1) and histone deacetylase 1 (HDAC1) that binds to and deacetylates these regions. These changes are not only maintained at the transcriptional level but also amplified, as most target regions are located near genes encoding transcription factors. CONCLUSIONS: We suggest that stochasticity in the histone deacetylation pathway participates in the generation of genetic-independent behavioral inter-individual variability.• Beca Juan de la Cierva, para Ángel Carlos Román García • Beca Federación de Sociedades Bioquímicas Europeas, para Ángel Carlos Román García • Beca predoctoral JAE-CSIC (España), para Julián Vicente Page • Contrato Ramón y Cajal RYC-2015-17867, para José María Carvajal González • Ministerio de Economía, y Competitividad. Proyectos BFU2014-54699-P (I+D+i) y BFU-2017-85547-P, para José María Carvajal González • Ministerio de Economía, y Competitividad. Proyectos BFU2011-22678 (I+D+i), para Pedro María Fernández Salguero • Ministerio de Economía, y Competitividad. Proyectos BFU2012-33448, para Gonzalo García de Polavieja Embid • Junta de Junta de Extremadura. Ayuda GR15164, para José María Carvajal González • Unión Europea. Iniciativa ERASysBio, apoyada en el marco del Espacio Europeo de Investigación (ERA-NET), en el marco Plus del Programa Marco 7, para Gonzalo García de Polavieja Embid • Fundaçao para a Ciência e Tecnologia. Proyecto PTDC/NEU-SCC/0948/2014, para Gonzalo García de Polavieja Embid • Champalimaud Fundación. Ayuda para Gonzalo García de Polavieja EmbidpeerReviewe

Targeting of CTCF to the nucleolus inhibits nucleolar transcription through a poly(ADP-ribosyl)ation-dependent mechanism

Multiple functions have been reported for the transcription factor and candidate tumour suppressor, CTCF. Among others, they include regulation of cell growth, differentiation and apoptosis, enhancer-blocking activity and control of imprinted genes. CTCF is usually localized in the nucleus and its subcellular distribution during the cell cycle is dynamic; CTCF was found associated with mitotic chromosomes and the midbody, suggesting different roles for CTCF at different stages of the cell cycle. Here we report the nucleolar localization of CTCF in several experimental model systems. Translocation of CTCF from nucleoplasm to the nucleolus was observed after differentiation of K562 myeloid cells and induction of apoptosis in MCF7 breast cancer cells. CTCF was also found in the nucleoli in terminally differentiated rat trigeminal ganglion neurons. Thus our data show that nucleolar localization of CTCF is associated with growth arrest. Interestingly, the 180 kDa poly(ADP-ribosyl)ated isoform of CTCF was predominantly found in the nucleoli fractions. By transfecting different CTCF deletion constructs into cell lines of different origin we demonstrate that the central zinc-finger domain of CTCF is the region responsible for nucleolar targeting. Analysis of subnucleolar localization of CTCF revealed that it is distributed homogeneously in both dense fibrillar and granular components of the nucleolus, but is not associated with fibrillar centres. RNA polymerase I transcription and protein synthesis were required to sustain nucleolar localization of CTCF. Notably, the labelling of active transcription sites by in situ run-on assays demonstrated that CTCF inhibits nucleolar transcription through a poly(ADP-ribosyl)ation-dependent mechanism

Conceptual Refactoring for Creative Information Retrieval

Information retrieval (IR) is an effective mechanism for text management that has received widespread adoption in the world at large. But it is not a particularly creative mechanism, in the sense of creating new conceptual structures or refactoring existing ones to pull in documents that describe, in novel and inventive ways, a user’s information needs. Since language is a dynamic and highly creative medium of expression, the concepts that one seeks will therefore represent a moving target for IR systems. We argue that only by thinking creatively, and viewing concepts as fluid meaning structures capable of dynamic reorganization, can an IR system effectively retrieve documents that express themselves creatively

Plant breeding for organic farming: current status and problems in Europe

Compendium is a part of Deliverable 4 of 6th FP SSA project “Environmental friendly food production system: requirements for plant breeding and seed production” (ENVIRFOOD) and contains information about current status and problems in EU regarding to organic plant breeding

Morphological and biological characteristics of the land races of the spring soft wheat grown in the organic farming system

Organic farmers have become more interested in the marginally grown (neglected) cultivars, as spring forms of the hulled wheat varieties (eincorn, emmer wheat, spelta wheat) or intermediate forms of the soft wheat. 173 land races from the gene bank at the RI in Praha-Ruzyně were grown on the organic certified parcel and evaluated in 2008. The trial aimed to evaluate the conditions of the competitiveness to weeds, tolerance to diseases, assimilation of the sun shine and establishment of the yield. The results show that all the evaluated material inclines to the competitiveness to weeds. This ability is, nevertheless, reduced because of the inclination to the lodging (all the cultivars have long weak stalks). Eincorn and emmer wheat are resistant to mildew and brown rust, spelta wheat is less resistant cultivar and the intermediate cultivars incline to disease attack very much. Eincorn and emmer wheat have short and dense spikes, spelta wheat has long and sparse spikes. Perspective materials have been found in the study and trials. We are going to focus on a possible increase of the resistance to lodging, choice of the resistant cultivars to funga diseases and increase of the spike productivity

Investigation of the use of histone deacetylase inhibitors for the treatment of inherited disorders of the glycolytic pathway

Histone acetylation by histone acetyltransferases (HATs) and deacetylation by histone deacetylases (HDACs) regulate gene expression by activating or repressing transcription, respectively. HDAC inhibitors (HDACIs) are a diverse class of drugs used to treat haemoglobinopathies, urea cycle disorders and several types of malignancies. Recent evidence from genome-wide as well as gene-specific epigenetic studies suggest a model whereby active genes are more likely than silent genes to be hyperacetylated and increase their transcription levels in response to HDACIs, a process underpinned by the dynamic recruitment and antagonistic activities of HATs and HDACs. Based on this model and from a therapeutic perspective, I hypothesised that the ability of HDACIs to increase expression of active genes might be relevant for diseases caused by genes that encode proteins with enzymatic function. HDACI-mediated increase in gene transcription, even in the presence of missense, disease-causing mutations, might lead to increased enzymatic activity and amelioration of the cellular and clinical phenotype. I tested this hypothesis on a group of genes involved in the glycolytic and pentose phosphate pathway (GPPP) which, when mutated, cause chronic or episodic haemolytic anaemia. Using RT-qPCR (B cell lines) and gene expression profiling (primary, in vitro generated human erythroid precursors and CD4+ T cells) I found that of the 17 GPPP genes, only Glucose-6-Phosphate Dehydrogenase (G6PD) mRNA levels increased in response to HDACIs in a time-dependent manner. Epigenetic analysis in B cells by ChIP-qPCR showed that histone hyper-acetylation and increased recruitment of HATs and HDACs underpin the selective G6PD transcriptional activation in response to HDACIs. Pharmacological and genetic assays showed that increase in G6PD transcription was also dependent on Sp1, a generic transcription factor known to recruit both HDACs and HATs. Finally, I directly tested the hypothesis that HDACIs may increase enzymatic activity in G6PD deficient cells. Using B cell lines and primary erythroid cells from patients with G6PD deficiency, I found that HDACIs induce the same epigenetic changes in the mutant as in the wild type G6PD gene; more importantly, they lead to increased levels of the mutant mRNA and protein, associated with an up to 3-fold increase in enzymatic activity. These findings are potentially of great therapeutic significance for correction of G6PD deficiency in up to 300 million individuals worldwide with the polymorphic variants of G6PD deficiency (e.g., G6PDMed and G6PDA-).Open Acces