| 1. |
- Delgado, Luis Fernando, et al.
(författare)
-
Phylogeny-based comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Vibrio vulnificus is a natural part of the microbiome of brackish waters worldwide. It is also an opportunistic pathogen that can cause severe infections and septicemia via consumption of seafood or through wound infections. The species possess diverse virulence factors, yet its precise disease mechanism remains undefined. Comparative genomics between clinical and environmental isolates offers a means to identify key virulence genes, but the scarcity of environmental isolates for V. vulnificus has constituted a significant limitation. Here we sequenced genomes of 82 V. vulnificus isolates from water, sediment and seagrass surface from stations along the Baltic Sea coast and complemented these with 208 and 117 previously sequenced clinical and environmental genomes, respectively, in a comparative analysis. Phylogenetic reconstruction corroborated earlier analysis with four main lineages forming within the species. Strains from the Baltic Sea region were confined to certain phylogenetic lineages (L4 and sublineages L2c and L2e) whereas clinical and environmental strains were found in all lineages, indicting that the phylogenetic structure of V. vulnificus reflects adaptations to specific environmental conditions rather than pathogenicity. Employing orthologue enrichment analysis in a phylogenetic framework using the PhyloBOTL pipeline developed in this work revealed 58 significantly enriched orthologs in clinical compared to environmental isolates. These orthologs were grouped into 18 co-localisation clusters based on the corresponding genes’ proximity in the genomes. The co-localisation clusters entailed clusters with 1 genes previously linked with pathogenicity in V. vulnificus, such as genes for capsular polysaccharide (CPS) synthesis and biofilm formation, but also clusters with genes not previously associated with virulence in the species. Examples of the latter were genes for pilus biosynthesis of the usher-chaperone (CU) pathway, for spermidine synthesis, and for effector proteins of the Type VI secretion system. Finally we leveraged on the clinically enriched genes to design PCR primers for detection and surveillance of pathogenic V. vulnificus strains.
|
|
| 2. |
- Ekeberg, Tomas, 1983-, et al.
(författare)
-
Three-dimensional structure determination with an X-ray laser
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus.
|
|
