Meningococcal genetic variation mechanisms viewed through comparative analysis of Serogroup C strain FAM18

Copyright @ 2007 Public Library of ScienceThe bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.This work was supported by the Wellcome Trust through the Beowulf Genomics Initiative

Chief digital officers:An analysis of the presence of a centralized digital transformation role

By appointing a chief digital officer (CDO), firms decide for a central role responsible for their digital transformation. While CDOs have recently appeared in the C-suites of firms across the globe, the current literature lacks insights into the specific antecedents of CDO presence. Grounded in the peculiarities of the digital age, we provide theoretical arguments explaining how the decision to centralize digital transformation responsibilities might be related to transformation urgency and coordination needs. Empirical analyses based on a panel data set of 913 U.S. and European firms support that transformation urgency and coordination needs predict CDO presence. An additional analysis of moderating temporal effects reveals that, over time, the effect of transformation urgency is weakened and the effect of coordination needs on CDO presence is strengthened. We discuss implications for research and practice regarding the antecedents of CDO presence, TMT research more generally, and centralization in the digital age

The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081

The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens

Connected components of spaces of Morse functions with fixed critical points

Let $M$ be a smooth closed orientable surface and $F=F_{p,q,r}$ be the space of Morse functions on $M$ having exactly $p$ critical points of local minima, $q\ge1$ saddle critical points, and $r$ critical points of local maxima, moreover all the points are fixed. Let $F_f$ be the connected component of a function $f\in F$ in $F$. By means of the winding number introduced by Reinhart (1960), a surjection $\pi_0(F)\to{\mathbb Z}^{p+r-1}$ is constructed. In particular, $|\pi_0(F)|=\infty$, and the Dehn twist about the boundary of any disk containing exactly two critical points, exactly one of which is a saddle point, does not preserve $F_f$. Let $\mathscr D$ be the group of orientation preserving diffeomorphisms of $M$ leaving fixed the critical points, ${\mathscr D}^0$ be the connected component of ${\rm id}_M$ in $\mathscr D$, and ${\mathscr D}_f\subset{\mathscr D}$ the set of diffeomorphisms preserving $F_f$. Let ${\mathscr H}_f$ be the subgroup of ${\mathscr D}_f$ generated by ${\mathscr D}^0$ and all diffeomorphisms $h\in{\mathscr D}$ which preserve some functions $f_1\in F_f$, and let ${\mathscr H}_f^{\rm abs}$ be its subgroup generated ${\mathscr D}^0$ and the Dehn twists about the components of level curves of functions $f_1\in F_f$. We prove that ${\mathscr H}_f^{\rm abs}\subsetneq{\mathscr D}_f$ if $q\ge2$, and construct an epimorphism ${\mathscr D}_f/{\mathscr H}_f^{\rm abs}\to{\mathbb Z}_2^{q-1}$, by means of the winding number. A finite polyhedral complex $K=K_{p,q,r}$ associated to the space $F$ is defined. An epimorphism $\mu:\pi_1(K)\to{\mathscr D}_f/{\mathscr H}_f$ and finite generating sets for the groups ${\mathscr D}_f/{\mathscr D}^0$ and ${\mathscr D}_f/{\mathscr H}_f$ in terms of the 2-skeleton of the complex $K$ are constructed.Comment: 12 pages with 2 figures, in Russian, to be published in Vestnik Moskov. Univ., a typo in theorem 1 is correcte

La pena de treballs en benefici de la comunitat : prevenció i gestió de les incidències en el seu compliment

Aquest estudi té com a objectiu explorar la prevenció i gestió d'incidències que duen a terme els delegats d'execució de mesures per tal d'aconseguir un compliment efectiu, per part dels penats a TBC. Així, a través del marc teòric es vol abordar el compliment en general per tal de comprendre la seva importància des de diferents perspectives així com els elements que la literatura científica mostra com a dificultats en el procés de compliment. El treball de camp recull les aportacions de delegades d'execució de mesures mitjançant una metodologia qualitativa.This study aims to explore the prevention and management of incidents carried out by probation officers aimed at the effective compliance, by those sentenced to community service. Thus, the theoretical framework aims to address compliance in general in order to understand its importance from different perspectives as well as the elements that the scientific literature shows as difficulties in the compliance process. The fieldwork collects the visions of probation officers using a qualitative methodology

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genomic reconstruction of the SARS-CoV-2 epidemic in England.

The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021