Genome Sequence of Fusobacterium nucleatum Subspecies Polymorphum — a Genetically Tractable Fusobacterium

Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common

Characterizing the Dynamics of Academic Affiliations: A Network Science Approach

Affiliation exchanges are inherent phenomena of academia that underlies some of the structural characteristics of academic institutions. Important questions involving the dynamics of institutions’ prestige, the concentration of funding, the spread of scientific ideas, and interdisciplinarity are all related to which institution academics will move upon completion of their training, or when looking for a better environment to pursue their research endeavors. In this work, we investigated the phenomena of affiliation switches in academia and its relationship with research topics in Computer Science. Drawing from publication data spanning over thirty years, we mapped the connections among academic institutions as networks. We report on the stability of network properties over the years in spite of the exponential growth of Computer Science in recent decades. Additionally, we contextualize the structural properties of networks and topic modeling results with the current academic landscape. Altogether, our results help to characterize the phenomena of academic affiliation exchanges through the macro perspective of network science and natural language processing