| 2. |
- Nilsson, Emelie, et al.
(author)
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Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341
- 2019
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In: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 85:18, s. 1-19
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Journal article (peer-reviewed)abstract
- Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of "unknowns" that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting Rheinheimem sp. strain BAL341 (Gammaproteobacteria) were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name Barbavirus. All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, phoH, and rnazG. One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages' replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system. IMPORTANCE Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring "kill-the-winner" oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems.
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| 3. |
- Staron, Miroslaw, 1977, et al.
(author)
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Identifying Implicit Architectural Dependencies using Measures of Source Code Change Waves
- 2013
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In: 39th Euromicro Conference Series on Software Engineering and Advanced Applications, SEAA 2013; Santander; Spain; 4 September 2013 through 6 September 2013. - 9780769550916 ; , s. 325-332
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Conference paper (peer-reviewed)abstract
- The principles of Agile software development are increasingly used in large software development projects, e.g. using Scrum of Scrums or combining Agile and Lean development methods. When large software products are developed by self-organized, usually feature-oriented teams, there is a risk that architectural dependencies between software components become uncontrolled. In particular there is a risk that the prescriptive architecture models in form of diagrams are outdated and implicit architectural dependencies may become more frequent than the explicit ones. In this paper we present a method for automated discovery of potential dependencies between software components based on analyzing revision history of software repositories. The result of this method is a map of implicit dependencies which is used by architects in decisions on the evolution of the architecture. The software architects can assess the validity of the dependencies and can prevent unwanted component couplings and design erosion hence minimizing the risk of post-release quality problems. Our method was evaluated in a case study at one large product at Saab Electronic Defense Systems (Saab EDS) and one large software product at Ericsson AB.
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