Computational Tools for Population Genomics

2018 ◽  
pp. 127-160 ◽  
Author(s):  
Jarkko Salojärvi
Keyword(s):  
Population Genomics ◽  
Computational Tools

Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence

2020 ◽  
pp. PHYTO-08-20-035
Author(s):  
Michael J. McLeish ◽  
Aurora Fraile ◽  
Fernando García-Arenal
Keyword(s):  
Multidisciplinary Approach ◽  
Population Genomics ◽  
Disease Risk ◽  
Plant Viruses ◽  
Computational Tools ◽  
Natural Systems ◽  
Large Numbers ◽  
Demographic Processes ◽  
Genetic Mechanisms ◽  
Virus Emergence

The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data. In this review, we discuss the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multidisciplinary approach to tackling disease risk. The ability to make sense of the information now generated in this integrated setting is by far the most substantial obstacle to the ultimate goal of plant virology to minimize the threats to food security posed by disease. To achieve this goal, it is imperative to understand and forecast how populations respond to future changes in complex natural systems.

Optical Properties of Photodynamic Therapy Drugs in Different Environments: The Paradigmatic Case of Temoporfin

2020 ◽  
Author(s):  
busenur Aslanoglu ◽  
Ilya Yakavets ◽  
Vladimir Zorin ◽  
Henri-Pierre Lassalle ◽  
Francesca Ingrosso ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Optical Properties ◽  
Photodynamic Therapy ◽  
Minimally Invasive ◽  
Visible Light ◽  
Cancer Treatment ◽  
Singlet Oxygen ◽  
Tumor Cells ◽  
Molecular Oxygen ◽  
Computational Tools

Computational tools have been used to study the photophysical and photochemical features of photosensitizers in photodynamic therapy (PDT) –a minimally invasive, less aggressive alternative for cancer treatment. PDT is mainly based by the activation of molecular oxygen through the action of a photoexcited sensitizer (photosensitizer). Temoporfin, widely known as mTHPC, is a second-generation photosensitizer, which produces the cytotoxic singlet oxygen when irradiated with visible light and hence destroys tumor cells. However, the bioavailability of the mostly hydrophobic photosensitizer, and hence its incorporation into the cells, is fundamental to achieve the desired effect on malignant tissues by PDT. In this study, we focus on the optical properties of the temoporfin chromophore in different environments –in <i>vacuo</i>, in solution, encapsulated in drug delivery agents, namely cyclodextrin, and interacting with a lipid bilayer.

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