Inferring Genetic Regulatory Networks Using Cost-based Abduction and Its Relation to Bayesian Inference

Inferring Genetic Regulatory Networks (GRN) from multiple data sources is a fundamental problem in computational biology. Computational models for GRN range from simple Boolean networks to stochastic differential equations. To successfully model GRN, a computational method has to be scalable and capable of integrating different biological data sources effectively and homogeneously. In this thesis, we introduce a novel method to model GRN using Cost-Based Abduction (CBA) and study the relation between CBA and Bayesian inference. CBA is an important AI formalism for reasoning under uncertainty that can integrate different biological data sources effectively. We use three different yeast genome data sources—protein-DNA, protein-protein, and knock-out data—to build a skeleton (unannotated) graph which acts as a theory to build a CBA system. The Least Cost Proof (LCP) for the CBA system fully annotates the skeleton graph to represent the learned GRN. Our results show that CBA is a promising tool in computational biology in general and in GRN modeling in particular because CBA knowledge representation can intrinsically implement the AND/OR logic in GRN while enforcing cis-regulatory logic constraints effectively, allowing the method to operate on a genome-wide scale.Besides allowing us to successfully learn yeast pathways such as the pheromone pathway, our method is scalable enough to analyze the full yeast genome in a single CBA instance, without sub-networking. The scalability power of our method comes from the fact that our CBA model size grows in a quadratic, rather than exponential, manner with respect to data size and path length. We also introduce a new algorithm to convert CBA into an equivalent binary linear program that computes the exact LCP for the CBA system, thus reaching the optimal solution. Our work establishes a framework to solve Bayesian networks using integer linear programming and high order recurrent neural networks through CBA as an intermediate representation.Ph

Sustainable production of Kochia indica grown in saline habitat

Abstract Biosaline agriculture is considered as unconventional approach for sustainable use of marginal soil (salt affected soils with poor drainage) and salt affected irrigation water. These can be used for planting non-traditional crops such as halophytic plants to overcome the serious shortage of fresh water and conventional soil. To achieve the aforementioned objectives, two field experiments were carried around Qaroon lake, Fayum Governorate, Egypt at the two successive summer season of 2011 -2012 to study the effect of foliar application of zinc, potassium or ascorbic acid in addition to fresh water as control on vegetative growth and some physiochemical parameters of Kochia indica grown under diluted saline water (Fresh water, 25% and 50%) from Qaroon Lake. Irrigation with 25% dilution significantly increased plant growth compared to fresh water irrigation. Raising irrigation salinity levels up to 50% significantly increase the content of chlorophyll a+b, proline, soluble carbohydrates and osmotic potential values compared to fresh water. On the other hand, the same treatment decreased the content of potassium and zinc in the shoot of K inica plant. However moderate saline irrigation i.e. 25 % generally increased crude protein content. All foliar spraying treatments significantly increased plant height, number of branched/plant, leaf area, shoot dry weight, root dry weight, chlorophyll a+b, crude protein, potassium and zinc as well as (salinity tolerance index) STI and succulence values as compared with control plants. On the other hand, foliar treatments decreased the content of soluble carbohydrates, proline and osmotic potential values. As for the interaction effect of between saline irrigation and foliar treatments, data show that the highest content of crude proten % and photosynthetic pigments were recorded in Kochia indica plants sprayed with 2% KNO 3 and irrigated with 25% Lake water, meanwhile plants sprayed with 300 ppm Zn-EDTA and irrigated with fresh water produced the highest zinc content. Furthermore, plants sprayed with fresh water and irrigated with 50% Lake water produced the highest content of soluble carbohydrates and proline as well as succulence and osmotic potential values. In conclusion, Foliar application with potassium surpasses all the other treatments especially under high levels of saline irrigation

Yield and nutrient status of wheat plants (Triticum aestivum) as affected by sludge, compost, and biofertilizers under newly reclaimed soil

Abstract Background Two field experiments were carried out during the two successive winter seasons of 2012–2013 and 2013–2014 in Research and Production Station, National Research Centre, Al-Nubaria District, Al-Behaira Governorate, Egypt. This work was carried out to study the effect of sludge and compost application combined with biofertilizers on yield and yield components as well as nutrient content of grains. Results The obtained results showed that either sludge or compost as organic fertilizers increased most yield parameters, i.e., spike length, weight of spike, and number and weight of grains per spike. Grain and straw yield as well as biological yield ton/faddan increased by either sludge or compost as compared with chemical fertilizers. Nutrient uptake of wheat grain increased also by both fertilizer and dual application with either sludge or compost with biofertilizers. Conclusion From the obtained results, it was revealed that application of compost or sludge with either "azotobacter" or yeast as biofertilizers has superior promoting effect on yield and yield components as well as nutrient content of the grains than chemical fertilizers. Thus, it can be recommended to substitute chemical fertilization by these organic and biofertilizers to obtain high productivity of wheat

Water Conservation Practices in Agriculture to Cope with Water Scarcity

Abstract: The increasingly demand for freshwater in last few decades, due to continued population growth and the direct impact of climate change, water supply limits and global warming, which leads to greater evaporation and thus surface drying, thereby increasing the intensity and duration of drought, especially in arid and semi-arid regions of the globe. In the coming decades, water experts are predicting more than half the world's population will suffer acute water scarcity by 2050. In order to avoid such a catastrophe, new habits and innovative technologies will be called upon to help the world's population to conserve and reuse existing sources of water. This concept is often described in terms such as sustainable water use, conservation, wateruse efficiency, water productivity, reducing water footprint, breeding for high water-use efficiency crops, sustainable use of saline and groundwater, shifting from flood irrigation to sprinkler and drip irrigation systems, improved irrigation scheduling, using local climate and soil information to help farmers more precisely irrigate to meet crop water needs and applying less water to crops during drought-tolerant growth stages to save water and improve crop quality or yield and use of smart irrigation systems. Unconventional approach is planting non-traditional crops such as halophytic forage crops (Leptochloa fusca, sporobolus virginicus, Kochia indica, Spartina patens, Kochia scoparia and Salicornia europeae). These plants have an economic value and can tolerate harvesting ten times per year and were capable of recovering and maintaining a reasonable fresh productive biomass and its cellulosic biomass can use for ethanol production. Successive cuttings of these halophytic plants improve soil quality, decrease SAR and electrical conductivity (dS/m) since some of these plants can accumulate salts into their leaves vacuoles. Growing these plants as multi-use crops for forage and biofuel production on salt affected land that can be irrigated with brackish water or seawater. Thus freeing fresh water for food and feed, contribute to energy security, guarantee environmental sustainability. Other options are development of new varieties of crops adapted to heat, salinity and drought with short growing season to reduce their water requirements. Modify the techniques of irrigation, including water quantity, timing of irrigation, technology i.e. improve crop management under limited amount of available water to maximize the return by unit of water (water productivity) to fit growing in arid and semi-arid regions to produce more crops per drop in a world with water shortage