Search results for "Bioinformatic"
showing 10 items of 1651 documents
Insects and fungi: ecological interactions and functional biodiversity
Identification and characterization of nitrate-related genes in durum wheat (Triticum turgidum L. subsp. durum Desf.) to improve Nitrogen Use Efficie…
2022
The increasing foods demand caused by the increasing world population posed new challenges to the modern agriculture. In recent years, many strategies have been adopted to cope with these needs and satisfy these demands. Among these, the improvement of agronomic techniques and plant selection and breeding are crucial for a sustainable improvement of crop production. Nitrogen (N) is an essential nutrient for plant growth and development due to its important role in several biochemical pathways, constituting 2-5 % of plant dry matter. The excessive use of N fertilizer led to high environmental pollution with impacts on both ecosystems and human health. Therefore, N inputs reduction is one of …
Transcriptome changes induced by Arbuscular mycorrhizal symbiosis in leaves of durum wheat (Triticum durum Desf.) promote higher salt tolerance
2022
AbstractThe salinity of soil is a relevant environmental problem around the world, with climate change raising its relevance, particularly in arid and semiarid areas. Arbuscular Mycorrhizal Fungi (AMF) positively affect plant growth and health by mitigating biotic and abiotic stresses, including salt stress. The mechanisms through which these benefits manifest are, however, still unclear. This work aimed to identify key genes involved in the response to salt stress induced by AMF using RNA-Seq analysis on durum wheat (Triticum turgidum L. subsp. durum Desf. Husn.). Five hundred sixty-three differentially expressed genes (DEGs), many of which involved in pathways related to plant stress resp…
MicroRNA Interaction Networks
2021
La tesi di Giorgio Bertolazzi è incentrata sullo sviluppo di nuovi algoritmi per la predizione dei legami miRNA-mRNA. In particolare, un algoritmo di machine-learning viene proposto per l'upgrade del web tool ComiR; la versione originale di ComiR considerava soltanto i siti di legame dei miRNA collocati nella regione 3'UTR dell'RNA messaggero. La nuova versione di ComiR include nella ricerca dei legami la regione codificante dell'RNA messaggero. Bertolazzi’s thesis focuses on developing and applying computational methods to predict microRNA binding sites located on messenger RNA molecules. MicroRNAs (miRNAs) regulate gene expression by binding target messenger RNA molecules (mRNAs). Therefo…
Mapreduce in computational biology - A synopsis
2017
In the past 20 years, the Life Sciences have witnessed a paradigm shift in the way research is performed. Indeed, the computational part of biological and clinical studies has become central or is becoming so. Correspondingly, the amount of data that one needs to process, compare and analyze, has experienced an exponential growth. As a consequence, High Performance Computing (HPC, for short) is being used intensively, in particular in terms of multi-core architectures. However, recently and thanks to the advances in the processing of other scientific and commercial data, Distributed Computing is also being considered for Bioinformatics applications. In particular, the MapReduce paradigm, to…
Mapreduce in computational biology via hadoop and spark
2017
Bioinformatics has a long history of software solutions developed on multi-core computing systems for solving computational intensive problems. This option suffer from some issues solvable by shifting to Distributed Systems. In particular, the MapReduce computing paradigm, and its implementations, Hadoop and Spark, is becoming increasingly popular in the Bioinformatics field because it allows for virtual-unlimited horizontal scalability while being easy-to-use. Here we provide a qualitative evaluation of some of the most significant MapReduce bioinformatics applications. We also focus on one of these applications to show the importance of correctly engineering an application to fully exploi…
Comparative genomics between two insect symbiotic models: Innate immune system and amino acid biosynthetic pathways of the rice weevil Sitophilus ory…
2019
Los insectos se pueden encontrar en la mayoría de los ecosistemas del planeta y son capaces de aprovechar prácticamente cualquier fuente de alimento. Son el grupo de animales más diverso con un número de especies estimado en cinco millones. Todos los insectos comparten un mismo plan corporal que consiste en tres segmentos (cabeza, tórax y abdomen), tres pares de patas, un par de antenas y ojos compuestos; sin embargo, cada especie tiene partes especializadas acordes con su estilo de vida. A pesar de que los insectos son capaces de aprovechar múltiples fuentes de alimento, en múltiples ocasiones dependen de compañeros microbianos para obtener nutrientes escasos en su dieta. Por ello, la simb…
Gene ontology-based annotation and comparative analysis of proteins extracted from proteomics of 100 breast cancer patients.
2009
Background: Current clinical parameters for breast cancer diagnosis and therapy are: tumour size, axillary lymph node status, histological grading and presence or absence of metastases. Prognostic/predictive properties, such as oestrogen and progesterone receptor status, and human epidermal growth factor receptor (HER-2/neu) status are currently used for therapeutic decision. Conversely, it is now emerging that the number of genetic mutations and epigenetic deregulations in cancer is far more higher than previously thought. Therefore, proteomic screening for differential protein expression in subsets of tumor samples is an essential tool for generating data bases and biomarker discovery. Th…
PathVisio Analysis: An Application Targeting the miRNA Network Associated with the p53 Signaling Pathway in Osteosarcoma
2021
MicroRNAs (miRNAs) are small single-stranded, non-coding RNA molecules involved in the pathogenesis and progression of cancer, including osteosarcoma. We aimed to clarify the pathways involving miRNAs using new bioinformatics tools. We applied WikiPathways and PathVisio, two open-source platforms, to analyze miRNAs in osteosarcoma using miRTar and ONCO.IO as integration tools. We found 1298 records of osteosarcoma papers associated with the word "miRNA". In osteosarcoma patients with good response to chemotherapy, miR-92a, miR- 99b, miR-193a-5p, and miR-422a expression is increased, while miR-132 is decreased. All identified miRNAs seem to be centered on the TP53 network. This is the first …