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Additional Remarks, Perspectives, and Conclusions
Published in Franklyn De Silva, Jane Alcorn, The Elusive Road Towards Effective Cancer Prevention and Treatment, 2023
Franklyn De Silva, Jane Alcorn
The ability to track and characterize the individual evolutionary trajectories of a carcinoma may aid in probing phylogenetic relationships and assist in the identification of predictive new biomarkers for personalized therapies [517]. Structured heterogeneity data can identify the common driver events shared by each and every tumor region as well as the heterogeneous somatic events in multiple tumor areas of a specific tumor [274]. Such data is incorporated into existing databases that allow the tracking of the evolutionary trajectories of a cancer in an individual patient (e.g., “CancerTracer”) [274]. The collection of such data creates an opportunity to predict the likely path of tumor progression, which will be indispensable for diagnostic, prognostic, and treatment purposes [1448]. For this, cancer progression models (CPMs) that utilize cross-sectional samples (e.g., data on genetic alterations) can be valuable tools for predicting cancer progression [1448]. The ability to track the evolutionary trajectories and phylogenetic relationships also will be facilitated by recent innovations in linking experimental omics methods with other molecular and clinical resources (e.g., bioimaging, electronic records) [1449].
The Journey through the Gene: a Focus on Plant Anti-pathogenic Agents Mining in the Omics Era
Published in Mahendra Rai, Chistiane M. Feitosa, Eco-Friendly Biobased Products Used in Microbial Diseases, 2022
José Ribamar Costa Ferreira-Neto, Éderson Akio Kido, Flávia Figueira Aburjaile, Manassés Daniel da Silva, Marislane Carvalho Paz de Souza, Ana Maria Benko-Iseppon
The knowledge generated by integrating omics data provides a better understanding of the organism’s complexity and how they use their genetic resources in developmental, survival and adaptation processes. This also allows evolutionary and phylogenetic inferences and development in several areas, including agriculture, biotechnology, medicine, environment, among others (for a review, see VanEmon 2016; Tebani et al. 2016; Tanveer et al. 2018).
Pathology and Research
Published in Jeremy R. Jass, Understanding Pathology, 2020
How do the specific attributes of the discipline of anatomical pathology lend themselves to the advance of medical research? The most general contribution has been to the systematic classification of disease known as nosology. This process begins with the arrangement of the many thousands of known diseases into logical groupings, rather like the phylogenetic classification of species of animals and plants. Diseases may be grouped according to the usual age, sex or race of affected subjects, by the part of the body that is most severely affected, or by the type of treatment that would be employed. Although such classifications might have some use, they all fail to place diseases within distinct, non-overlapping boundaries. To achieve a more meaningful approach to nosology, it is necessary to look at the fundamental nature of a disease, specifically the mechanisms underlying its causation (aetiology) and evolution (pathogenesis).
Testing for genetic mutation of seasonal influenza virus
Published in Journal of Applied Statistics, 2023
Phylogeny is concerned with the evolution of groups and specifically about the lines of descent and relationships among groups. It is one of the best tools for understanding the evolution of pathogens. A phylogenetic tree is a diagram depicting a phylogeny through lines of evolutionary descent from a common ancestor. Throughout this article, the phrase ‘phylogenetic tree’ and ‘evolutionary tree’ are used interchangeably. Influenza viruses are permanently changing, undergoing genetic changes over time and monitoring these changes in the genome is fundamental to the production of vaccines on a seasonal basis. The RNA genes of influenza are made up of nucleotides. It is the composition of these nucleotides and the differences which account for the different viruses. The differences and ancestry of viruses are demonstrated through the use of a phylogenetic tree. The tree shows how different viruses are related to each other and are grouped together based on how close their corresponding nucleotides are. Specifically the phylogenetic trees of influenza viruses will usually display how similar the viruses hemagglutinin (HA) or neuraminidase (NA) genes are to one another. The tree consists of branches and branch lengths. Groups on the same branch share the same nucleotides. At a split of a branch, the length of the branch indicates how different (i.e. the number of nucleotide differences) from each other the groups are.
Identification, characterization, and molecular phylogeny of scorpion enolase (Androctonus crassicauda and Hemiscorpius lepturus)
Published in Toxin Reviews, 2023
Elham Pondehnezhadan, Atefeh Chamani, Fatemeh Salabi, Reihaneh Soleimani
The evolutionary origin and relevance of scorpions have been the subject of many studies in recent decades, especially recent pan-genome studies that support the Arachnopulmonata hypothesis: a sister-group relationship between scorpions and tetrapulmonates (i.e. spiders and allied orders) (Regier et al. 2010, Sharma et al. 2014, 2015). Previous morphological-based phylogenetic approaches are restricted to those scorpions exemplifying morphological stasis (Prendini and Wheeler 2005, Prendini et al. 2006). To address this challenge, however, phylogenetic relationships can be inferred more precisely using both molecular and morphological methods (Chippaux and Goyffon 2008). Molecular phylogeny compares homologous DNA or protein sequences to decide the relationships among organisms or genes. It constructs a hierarchical phylogenetic tree based on the genetic divergences of the similarity or dissimilarity of homologous molecules from different organisms, resulting from molecular evolution over time (Patwardhan et al. 2014).
Integration of network pharmacology and intestinal flora to investigate the mechanism of action of Chinese herbal Cichorium intybus formula in attenuating adenine and ethambutol hydrochloride-induced hyperuricemic nephropathy in rats
Published in Pharmaceutical Biology, 2022
Na Li, Mukaram Amatjan, Pengke He, Boheng Zhang, Xianyan Mai, Qianle Jiang, Haochen Xie, Xiaoni Shao
In our study, LEfse analysis (Segata et al. 2011) was adopted to seek biomarkers with statistically significant differences (LDA score > 4). As shown in Figure 10A, the main microbial species that differed between CG and other groups were Ruminococcaceae, Ruminococcaceae_UCG_005, Ruminococcaceae_UCG_014, Clostridiales and Clostridia. The main microbial species that differed between FHG and other groups were Bacteria. The main microbial species that differed between FLG and other taxa were Allobaculum, Erysipelotrichaceae, Bifidobacteriales, Bifidobacteriaceae, Erysipelotrichales, Erysipelotrichia, Catenibacterium, Bifidobacterium, Actinobacteria, Actinobacteria. An evolutionary diagram was shown in Figure 10B to demonstrate the distribution patterns of phylogenetic relationships for species that play an important role in each group. The functional prediction results of enrichment at three different levels of the ko metabolic pathway were shown in Figures 10C–E.