Collected results on semigroups, graphs and codes

In this thesis we present a compendium of _ve works where discrete mathematics play a key role. The _rst three works describe di_erent developments and applications of the semigroup theory while the other two have more independent topics. First we present a result on semigroups and code e_ciency, where we introduce our results on the so-called Geil-Matsumoto bound and Lewittes' bound for algebraic geometry codes. Following that, we work on semigroup ideals and their relation with the Feng-Rao numbers; those numbers, in turn, are used to describe the Hamming weights which are used in a broad spectrum of applications, i.e. the wire-tap channel of type II or in the t-resilient functions used in cryptography. The third work presented describes the non-homogeneous patterns for semigroups, explains three di_erent scenarios where these patterns arise and gives some results on their admissibility. The last two works are not as related as the _rst three but still use discrete mathematics. One of them is a work on the applications of coding theory to _ngerprinting, where we give results on the traitor tracing problem and we bound the number of colluders in a colluder set trying to hack a _ngerprinting mark made with a Reed-Solomon code. And _nally in the last work we present our results on scientometrics and graphs, modeling the scienti_c community as a cocitation graph, where nodes represent authors and two nodes are connected if there is a paper citing both authors simultaneously. We use it to present three new indices to evaluate an author's impact in the community

Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

Acknowledgements The authors would like to thank Mr Kevin Mackenzie and Mrs Gillian Milne (University of Aberdeen) for technical support with scanning electron microscopy, and Dr Robin Walker for access to the Woodlands Field experimental plots at the SRUC,Craibstone Estate, Aberdeen. Funding This work was financially supported by Natural Environmental Research Council (standard grants NE/I027835/1 and NE/L006286/1 and fellowship NE/J019151/1), EC Marie Curie ITN NORA, Grant Agreement No. 316472, the AXA Research Fund and the Centre for Genome Enabled Biology and Medicine, University of Aberdeen.Peer reviewedPublisher PD

In silico and in vitro-guided identification of inhibitors of alkylquinolone-dependent quorum sensing in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a major opportunistic pathogen in cystic fibrosis, wound and nosocomial infections, posing a serious burden to public health, due to its antibiotic resistance. The P. aeruginosa Pseudomonas Quinolone System (pqs) quorum sensing system, driven by the activation of the transcriptional regulator, PqsR (MvfR) by alkylquinolone (AQ) signal molecules, is a key player in the regulation of virulence and a potential target for the development of novel antibacterial agents. In this study, we performed in silico docking analysis, coupled with screening using a P. aeruginosa mCTX::PpqsA-lux chromosomal promoter fusion, to identify a series of new PqsR antagonists. The hit compounds inhibited pyocyanin and alkylquinolone signal molecule production in P. aeruginosa PAO1-L and PA14 strains. The inhibitor Ia, which showed the highest activity in PA14, reduced biofilmformation in PAO1-L and PA14, increasing their sensitivity to tobramycin. Furthermore, the hepatic and plasma stabilities for these compounds were determined in both rat and human in vitro microsomal assays, to gain a further understanding of their therapeutic potential. This work has uncovered a new class of P. aeruginosa PqsR antagonists with potential for hit to lead optimisation in the search for quorum sensing inhibitors for future anti-infective drug discovery programs

Architecture for the heterogeneous federation of future internet experimentation facilities

International audienceInternet systems are currently too complex to be entirely designed in advance and therefore must be thoroughly evaluated in realistic environments. Experimentally driven research is at the heart of Future Internet Research and Experiment (FIRE) facilities, which target various experimenter profiles, ranging from core Internet communities and sensor networks to clouds and web services. Such facilities exist in relative isolation to the detriment of innovative research ideas that could arise from the mixture of their diverse technologies and resources, and their combined power. Internet research communities can benefit from gaining access to a larger number and variety of resources through a federation of these facilities. To this end, we present an architecture to support such a federation of Future Internet experimentation facilities, based on use cases and requirements from infrastructure owners, as well as services and first line support communities

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics

Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. Acknowledgements We would like to thank Dr Robert Griffith/CEH for providing DNA from soil samples and Dr Anthony Travis for his help with BioLinux. Sequencing was performed in NERC platform in Liverpool. CG-R was funded by a NERC fellowship NE/J019151/1. CQ was funded by a MRC fellowship (MR/M50161X/1) as part of the cloud infrastructure for microbial genomics consortium (MR/L015080/1).Peer reviewedPublisher PD

Molecular adaptation of ammonia monooxygenase during independent pH specialization in Thaumarchaeota

Acknowledgements This work was funded by Natural Environment Research Council Fellowship NE/J019151/1 and by institutional funding from within the University of Aberdeen. Both authors designed and performed the research, analysed data and equally contributed to the writing of the manuscript.Peer reviewedPublisher PD