Fallacy of the unique genome: sequence diversity within single Helicobacter pylori strains

Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion in cagY, which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB -1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains

Fallacy of the unique genome: sequence diversity within single Helicobacter pylori strains

Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion in cagY, which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB -1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains

The structural basis of interlamellar cohesion in the intervertebral disc wall

The purpose of this study was to investigate the structural mechanisms that create cohesion between the concentric lamellae comprising the disc annulus. Sections, 50–60 µm thick, were obtained using a carefully chosen cutting plane that incorporated the fibrous component in alternating lamellae as in-plane and cross-sectioned arrays. These sections were then subjected to microtensile stretching both across (radial) and along (tangential) the in-plane fibre direction, in their fully hydrated state. Structural responses were studied by simultaneously viewing the sections using high-resolution Nomarski interference contrast light microscopy. Additional bulk samples of annulus were fixed while held in a constant, radially stretched state in order to investigate the potential for interlamellar separation to occur in a state more representative of the intact disc wall. The study has provided a detailed picture of the structural architecture creating disc wall cohesion, revealing a complex hierarchy of interconnecting relationships within the disc wall, not previously described. Importantly, because our experimental approach offers a high-resolution view of the response of the interlamellar junction to deformation in its fully hydrated condition, it is a potentially useful method for investigating subtle changes in junction cohesion resulting from both early degeneration and whole-disc trauma

The influence of torsion on disc herniation when combined with flexion

The role of torsion in the mechanical derangement of intervertebral discs remains largely undefined. The current study sought to investigate if torsion, when applied in combination with flexion, affects the internal failure mechanics of the disc wall when exposed to high nuclear pressure. Thirty ovine lumbar motion segments were each positioned in 2° axial rotation plus 7° flexion. Whilst maintained in this posture, the nucleus of each segment was gradually injected with a viscous radio-opaque gel, via an injection screw placed longitudinally within the inferior vertebra, until failure occurred. Segments were then inspected using micro-CT and optical microscopy in tandem. Five motion segments failed to pressurize correctly. Of the remaining 25 successfully tested motion segments, 17 suffered vertebral endplate rupture and 8 suffered disc failure. Disc failure occurred in mature motion segments significantly more often than immature segments. The most common mode of disc failure was a central posterior radial tear involving a systematic annulus–endplate–annulus failure pattern. The endplate portion of these radial tears often propagated contralateral to the direction of applied axial rotation, and, at the lateral margin, only those fibres inclined in the direction of the applied torque were affected. Apart from the 2° of applied axial rotation, the methods employed in this study replicated those used in a previously published study. Consequently, the different outcome obtained in this study can be directly attributed to the applied axial rotation. These inter-study differences show that when combined with flexion, torsion markedly reduces the nuclear pressure required to form clinically relevant radial tears that involve cartilaginous endplate failure. Conversely, torsion appears to increase the disc wall’s resistance to radial tears that do not involve cartilaginous endplate failure, effectively halving the disc wall’s overall risk of rupture