Phage therapy: A software system for phage quantification and kinetic model inference.

One of the most serious problems of the modern medicine is the growing emergence of antibiotic resistance among pathogenic bacteria. In this circumstance, different and innovative approaches for treating infections caused by multidrug-resistant bacteria are imperatively required. Bacteriophage Therapy is one among the fascinating approaches to be taken into account. This consists of the use of bacteriophages, viruses that infect bacteria, in order to defeat specific bacterial pathogens. Phage therapy is not an innovative idea, indeed, it was widely used around the world in the 1930s and 1940s, in order to treat various infection diseases, and it is still used in Eastern Europe and the former Soviet Union. Nevertheless, Western scientists mostly lost interest in further use and study of phage therapy and abandoned it after the discovery and the spread of antibiotics. The advancement of scientific knowledge of the last years, together with the encouraging results from recent animal studies using phages to treat bacterial infections, and above all the urgent need for novel and effective antimicrobials, have given a prompt for additional rigorous researches in this field. In particular, in the laboratory of synthetic biology of the department of Life Sciences at the University of Warwick, a novel approach was adopted, starting from the original concept of phage therapy, in order to study a concrete alternative to antibiotics. The innovative idea of the project consists in the development of experimental methodologies, which allow to engineer a programmable synthetic phage system using a combination of directed evolution, automation and microfluidics. The main aim is to make “the therapeutics of tomorrow individualized, specific, and self-regulated” (Jaramillo, 2015). In this context, one of the most important key points is the Bacteriophage Quantification. Therefore, in this research work, a mathematical model describing complex dynamics occurring in biological systems involving continuous growth of bacteriophages, modulated by the performance of the host organisms, was implemented as algorithms into a working software using MATLAB. The developed program is able to predict different unknown concentrations of phages much faster than the classical overnight Plaque Assay. What is more, it gives a meaning and an explanation to the obtained data, making inference about the parameter set of the model, that are representative of the bacteriophage-host interaction.

The nematode parasite fauna in three odontocete species: Phocoena phocoena, Lagenorhynchus albirostris, Lagenorhynchus acutus from Northern Scotland and its relationships with diet composition

Food items and nematode parasites were identified from the stomachs of 42 individuals of Phocoena phocoena, 6 of Lagenorhynchus acutus and 8 of L. albirostris stranded off the coastal waters of Northern Scotland between 2004 and 2014. Post-mortem examinations have revealed heavy parasitic worm burdens. Four nematode species complex as Anisakis spp., Contracaeucum spp., Pseudoterronova spp., and Hysterothylacium spp. were recorded. Data on presence of the anisakid species in cetaceans, reported a significative relationship between the presence of Hysterothylacium and the month of host stranding; suggesting a decrease of larval H. aduncum abundance in the period between April and August due to a seasonal effect related to prey availability. Similarly, the parasite burden of the all anisakid genera was related to the year fraction of stranding, and a relationship statistically significant was found just for L. albirostris with an increase between April and October. This finding is explained by a seasonality in occurrence of white-beaked dolphins, with a peak during August, that might be related to movements of shared prey species and competition with other species (Tursiops truncatus). Geographical differences were observed in parasites number of all anisakid species, which was the highest in cetaceans from the East area and lowest in the North coast. The parasites number also increased significantly with the length of the animal and during the year, but with a significant seasonal pattern only for P. phocoena. Regarding diet composition, through a data set consisting of 34 harbour porpoises and 1 Atlantic white-sided dolphins, we found a positive association between parasite number and the cephalopods genus Alloteuthis. This higher level of parasite infection in squid from this area, is probably due to a quantitative distribution of infective forms in squid prey, an abundance of the final host and age or size maturity of squid.