Identification of in silico mirnas in four plant species from fabaceae family

Plant microRNAs (miRNAs) are small non-coding RNAs, about 21-24 nucleotides, which have critical regulatory roles on growth, development, metabolic and defense processes. Their identification, together with their targets, have gained importance in exploring their parts on functional context, providing a better understanding of their regulatory roles in critical biological processes. With the advent of next-generation sequencing technologies and newly developed bioinformatics tools, the identification of microRNA studies by computational methods has been increasing. In the presented study, we identified some putative miRNAs for Cicer arietinum, Glycine max, Medicago truncatula and Phaseolus vulgaris genomes. We also provided the similarity between those organisms regarding common/different miRNAs availability throughout their genomes. According to the data, the highest similarity was found between Glycine max and Phaseolus vulgaris. We also investigated the potential targets of putatively identified miRNAs for each organism. We analyzed which miRNA families were expressed in silico. We also showed the representation (copy number of genes) profile of predicted putative miRNAs for each organism. Since most of the food products and animal feeds consist of Fabaceae family members as it is mentioned above, these findings might help to elucidate their metabolic and regulatory pathways to use them efficiently in biotechnological applications and breeding programs

Parallelized neural network system for solving Euclidean traveling salesman problem

We investigate a parallelized divide-and-conquer approach based on a self-organizing map (SOM) in order to solve the Euclidean Traveling Salesman Problem (TSP). Our approach consists of dividing cities into municipalities, evolving the most appropriate solution from each municipality so as to find the best overall solution and, finally, joining neighborhood municipalities by using a blend operator to identify the final solution. We evaluate the performance of parallelized approach over standard TSP test problems (TSPLIB) to show that our approach gives a better answer in terms of quality and time rather than the sequential evolutionary SOM

In silico analysis of MicroRNAs in spinacia oleracea genome and transcriptome

Plant microRNAs (miRNAs) are small non-coding RNAs, about 21-24 nucleotides, which have important regulatory roles in growth, development, metabolic and defense processes. These critical elements regulate pathways either by inducing translational repression or messenger RNA (mRNA) decay. With the advent of the next-generation sequencing technologies and newly developed bioinformatics tools, the identification of microRNA studies by computational methods have been increased. Thus, the sequencing information provides us information for mining some known and unknown miRNAs in plants. In this study, we predict 34 putative miRNAs from Spinacia oleracea genome and two putative miRNA families from spinach transcriptome by using homology-based conservation method. RepeatMasker program is utilized to mask and eliminate five miRNA families out of 34 putative miRNA families from spinach genome. Finally, we analyze the targets of putatively identified miRNAs and their representation of genes (the copy number of each miRNA) throughout the genome

TSP solver: an integrated framework for solving traveling salesman problems consistent with TSPLIB

The Traveling Salesman Problem (TSP) is the subject of study in operational research for more than 30 years. The TSP is considered as NP-complete; consequently, many heuristic and metaheuristic algorithms have been developed to cope with the intractable nature of the problem. Although the problem is well-studied, lack of integrated software that harnesses the new computers' computational power and provides an easy comparison between heuristic algorithms is sensible. TSP solver is the state-of-the-art software that provides a common framework to compare the performance of different algorithms over TSPLIB library. Academicians can focus on developing new methodologies without concerning the availability and correctness of reported algorithms in the literature. Practitioners may also benefit from provided transparency by our software solution and build their own customized packages to flourish their businesses. The proposed software can be a foundation for the future implementations in which users design their algorithm and results would be uploaded automatically on a public server together with the source code

Introgression of drought related QTLs into elite cultivars

In this study, we aimed to introgress drought related genomic regions identified in two South Australian cultivars into five European elite cultivars. We performed all different possible combinations of crosses. We confirmed the successful introgression of the drought related key regions in seven F1 plants using linked SSR markers. These plants were backcrossed three times until BC3F2, which will be extensively characterized for their yield components and water use efficiency under water limited conditions. With this research, we aim to develop bread wheat cultivars with high field performance in drought prone environments

Plant abiotic stress signaling

Stress signaling is central to plants which—as immobile organisms—have to endure environmental fluctuations that constantly interfere with vigorous growth. As a result, plant-specific, elaborate mechanisms have evolved to perceive and respond to stress conditions. Currently, these stress responses are plausibly being revealed to involve crosstalks with energy signaling pathways as any growth-limiting factor alters plant’s energy status. Among these, autophagy, conventionally regarded as the mechanism whereby plants recycle and remobilize nutrients in bulk, has frequently been associated with stress responses. With the recent discoveries, however, autophagy has attained a novel role in stress signaling. In this review, major elements of abitoic stress signaling are summarized along with autophagy pathway, and in the light of recent discoveries, a putative, state-of-art role of autophagy is discussed