The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae , the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for ≈80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.

We present the results of a molecular dynamics computer simulation study in which we investigate whether a supercooled Lennard-Jones liquid exhibits dynamical heterogeneities. We evaluate the non-Gaussian parameter for the self part of the van Hove correlation function and use it to identify “mobile” particles. We find that these particles form clusters whose sizes grow with decreasing temperature. We also find that the relaxation time of the mobile particles is significantly shorter than that of the average particle, and that this difference increases with decreasing temperature.

Extensive molecular dynamics simulations are performed on a glass-forming Lennard-Jones mixture to determine the nature of the cooperative motions occurring in this model fragile liquid. We observe stringlike cooperative molecular motion (“strings”) at temperatures well above the glass transition. The mean length of the strings increases upon cooling, and the string length distribution is found to be nearly exponential.

Using extensive molecular dynamics simulations of an equilibrium, glass-forming Lennard-Jones mixture, we characterize in detail the local atomic motions. We show that spatial correlations exist among particles undergoing extremely large (“mobile”) or extremely small (“immobile”) displacements over a suitably chosen time interval. The immobile particles form the cores of relatively compact clusters, while the mobile particles move cooperatively and form quasi-one-dimensional, stringlike clusters. The strength and length scale of the correlations between mobile particles are found to grow strongly with decreasing temperature, and the mean cluster size appears to diverge near the mode-coupling critical temperature. We show that these correlations in the particle displacements are related to equilibrium fluctuations in the local potential energy and local composition.

Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group.