Browsing by Author "Pereira, Ana Rita"
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- Environmental epigenetics and Daphnia as a model organismPublication . Pereira, Ana Rita; Silva, Regina; Barros, PiedadeDaphnia’s cyclic parthenogenesis life cycle is controlled by environmental cues and determines the population genetic variability. The asexual reproduction maintains the genetic background. This, allied to the fact that epigenetic changes were already described in Daphnia turns it in a useful model to study the effect of epigenetic changes in the organism.
- Salivary alpha-amylase activity variation along the menstrual cyclePublication . Pereira, Ana Rita; Frutuoso, JoséSalivary alpha-amylase, produced by the salivary glands, is the main enzyme present in saliva (Ekström, Khosravani, Castagnola, & Messana, 2012). The salivary glands and salivary alpha-amylase production can be influenced by many factors, including circadian rhythms, sex, age, stress, medication, tobacco and alcohol, as well as menstrual cycle (Alagendran, Archunan, Armando, & Guzman, 2010; Rohleder & Nater, 2009). There are reports of the inefficacy of saliva from menstruated women to digest glycogen in histochemical stains. However papers studying the relationship between salivary alpha-amylase activity and the menstrual cycle do not have consensual results.
- Sequence alignment: Comparative analysis of algorithms in KRAS genetic mutationsPublication . Pereira, Ana Rita; Lopes, Carlos; Oliveira, Catarina; Pereira, Gonçalo; Moreira, Rui; Faria, Brígida Mónica; Faria, Brigida MonicaFor this study a program was developed in Python on biological sequence alignment, considering the application of algorithms in the genetic analysis of Kristen rat sarcoma viral oncogene (KRAS) and its main mutations associated with cancer. The KRAS gene, like other genes in the same family, is responsible for encoding proteins that regulate cell proliferation, differentiation, and apoptosis. The algorithms employed include the Needleman-Wunsch algorithm as well as the Smith-Waterman algorithm and the Basic Local Alignment Search Tool (BLAST). The algorithms for multiple sequence alignment help to understand the function, evolution, and variability of biological sequences, significantly contributing to advances in genomics and proteomics. The objectives of this study are to apply algorithms for the effective alignment of biological sequences, compare the non-mutated KRAS sequence with principal mutations associated with cancer development, delineate and justify the selection of the algorithms used, assess their computational complexity, and facilitate 3D visualization of the sequences. Development of a program - BioAlign - in Python, with various functions including upload and visualization of sequences; use of different algorithms for global and local alignment; BLAST search; algorithms complexity analysis; obtaining the nucleotides positions; obtaining subsequence and its position; phylogenetic analysis; histogram visualization of sequence length and 3D structure visualization. The program is capable of analyzing and comparing the provided sequences using both local and global algorithms. The execution time among the three main algorithms differs, with the BLAST algorithm notably slower in returning results. This fact may be due to several factors, such as the complexity of the algorithm itself, the internet speed, and the response time of the NCBI website. The development of the BioAlign program indeed allows to address the proposed objectives. Furthermore, the completion of this project has enhanced proficiency in utilizing the Python programming language, demonstrating significant skill development.