Defining bacterial species in the genomic era : insights from the genus Acinetobacter

Background: Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. Results: In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. Conclusion: We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical

Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine

Streptococcus pneumoniae causes invasive infections, primarily at the extremes of life. A seven-valent conjugate vaccine (PCV7) is used to protect against invasive pneumococcal disease in children. Within three years of PCV7 introduction, we observed a fourfold increase in serotype 6C carriage, predominantly due to a single clone. We determined the whole-genome sequences of nineteen S. pneumoniae serotype 6C isolates, from both carriage (n = 15) and disease (n = 4) states, to investigate the emergence of serotype 6C in our population, focusing on a single multi-locus sequence type (MLST) clonal complex 395 (CC395). A phylogenetic network was constructed to identify different lineages, followed by analysis of variability in gene sets and sequences. Serotype 6C isolates from this single geographical site fell into four broad phylogenetically distinct lineages. Variation was seen in the 6C capsular locus and in sequences of genes encoding surface proteins. The largest clonal complex was characterised by the presence of lantibiotic synthesis locus. In our population, the 6C capsular locus has been introduced into multiple lineages by independent capsular switching events. However, rapid clonal expansion has occurred within a single MLST clonal complex. Worryingly, plasticity exists within current and potential vaccine-associated loci, a consideration for future vaccine use, target selection and design

Thomas–Fermi–Dirac–von Weizsäcker models in finite systems

To gain an understanding of the variational behavior of kinetic energy functionals, we perform a numerical study of the Thomas–Fermi–Dirac–von Weizsäcker theory in finite systems. A general purpose Gaussian-based code is constructed to perform energy and geometry optimizations on polyatomic systems to high accuracy. We carry out benchmark studies on atomic and diatomic systems. Our results indicate that the Thomas–Fermi–Dirac–von Weizsäcker theory can give an approximate description of matter, with atomic energies, binding energies, and bond lengths of the correct order of magnitude, though not to the accuracy required of a qualitative chemical theory. We discuss the implications for the development of new kinetic functionals

Correlation potentials and functionals in Hartree-Fock-Kohn-Sham theory

We compute molecular Hartree-Fock-Kohn-Sham correlation potentials from ab initiocoupled-cluster densities via a modified Zhao, Morrison and Parr [Phys. Rev. A, 50, (1994) 2138] scheme involving exact exchange. We examine the potential for several small systems, and observe complex structure. By fitting a functional expansion to our potentials we obtain a closed-shell functional which is an improvement over other pure correlationfunctionals in Hartree-Fock-Kohn-Sham calculations. The leading term in our functional is dependent on the number of electrons. Our results lead us to question the utility of correlation defined within the Hartree-Fock-Kohn-Sham scheme, and to consider alternative partitionings of the exchange-correlation energy

A copper-catalyzed asymmetric oxime propargylation enables the synthesis of the gliovirin tetrahydro-1,2-oxazine core

The bicyclic tetrahydro-1,2-oxazine subunit of gliovirin is synthesized through a diastereoselective copper-catalyzed cyclization of an N-hydroxyamino ester. Oxidative elaboration to the fully functionalized bicycle was achieved through a series of mild transformations. Central to this approach was the development of the first catalytic, enantioselective propargylation of an oxime to furnish a key N-hydroyxamino ester intermediate

Crosslinked Polypeptide Films via RAFT-Mediated Continuous Assembly of Polymers

Polypeptide coatings are a cornerstone in the field of surface modification due to their widespread biological potential. As their properties are dictated by their structural features, subsequent control thereof using unique fabrication strategies is important. Herein, we report a facile method of precisely creating densely crosslinked polypeptide films with unusually high random coil content through continuous assembly polymerization via reversible addition–fragmentation chain transfer (CAP‐RAFT). CAP‐RAFT was fundamentally investigated using methacrylated poly‐l‐lysine (PLLMA) and methacrylated poly‐l‐glutamic acid (PLGMA). Careful technique refinement resulted in films up to 36.1±1.1 nm thick which could be increased to 94.9±8.2 nm after using this strategy multiple times. PLLMA and PLGMA films were found to have 30–50 % random coil conformations. Degradation by enzymes present during wound healing reveals potential for applications in drug delivery and tissue engineering

Securities trading of concepts (STOC)

Identifying winning new product concepts can be a challenging process that requires insight into private consumer preferences. To measure consumer preferences for new product concepts, the authors apply a “securities trading of concepts,” or STOC, approach, in which new product concepts are traded as financial securities. The authors apply this method because market prices are known to efficiently collect and aggregate private information regarding the economic value of goods, services, and firms, particularly when trading financial securities. This research compares the STOC approach against stated-choice, conjoint, constant-sum, and longitudinal revealed-preference data. The authors also place STOC in the context of previous research on prediction markets and experimental economics. Across multiple product categories, the authors test whether STOC (1) is more cost efficient than other methods, (2) passes validity tests, (3) measures expectations of others, and (4) reveals individual preferences, not just those of the crowd. The results show that traders exhibit a self-preference bias when trading. Ultimately, STOC offers two key advantages over traditional market research methods: cost efficiency and scalability. For new product development teams deciding how to invest resources, this scalability may be especially important in the Web 2.0 world.United States. Office of Naval Research (Contract Number N00014-93-1-3085)National Science Foundation (U.S.). Information Technology Research (Contract Number IIS-0085836)National Science Foundation (U.S.). Knowledge and Distributed Intelligence Initiative (Contract Number DMS-9872936)National Science Foundation (U.S.) (Contract Number IIS-9800032)United States. Office of Naval Research (United States. Defense Advanced Research Projects Agency) (Contract Number N00014-00-1-0907

Rapid Additive-Free Selenocystine–Selenoester Peptide Ligation

We describe an unprecedented reaction between peptide selenoesters and peptide dimers bearing N-terminal selenocystine that proceeds in aqueous buffer to afford native amide bonds without the use of additives. The selenocystine-selenoester ligations are complete in minutes, even at sterically hindered junctions, and can be used in concert with one-pot deselenization chemistry. Various pathways for the transformation are proposed and probed through a combination of experimental and computational studies. Our new reaction manifold is also showcased in the total synthesis of two proteins

Calpain 2 and PTP1B function in a novel pathway with Src to regulate invadopodia dynamics and breast cancer cell invasion

Invasive cancer cells form dynamic adhesive structures associated with matrix degradation called invadopodia. Calpain 2 is a calcium-dependent intracellular protease that regulates adhesion turnover and disassembly through the targeting of specific substrates such as talin. Here, we describe a novel function for calpain 2 in the formation of invadopodia and in the invasive abilities of breast cancer cells through the modulation of endogenous c-Src activity. Calpain-deficient breast cancer cells show impaired invadopodia formation that is rescued by expression of a truncated fragment of protein tyrosine phosphatase 1B (PTP1B) corresponding to the calpain proteolytic fragment, which indicates that calpain modulates invadopodia through PTP1B. Moreover, PTP1B activity is required for efficient invadopodia formation and breast cancer invasion, which suggests that PTP1B may modulate breast cancer progression through its effects on invadopodia. Collectively, our experiments implicate a novel signaling pathway involving calpain 2, PTP1B, and Src in the regulation of invadopodia and breast cancer invasion

Construction of challenging proline–proline junctions via diselenide–selenoester ligation chemistry

Polyproline sequences are highly abundant in prokaryotic 10 and eukaryotic proteins, where they serve as key components of 11 secondary structure. To date, construction of the proline−proline motif 12 has not been possible owing to steric congestion at the ligation junction, 13 together with an n → π* electronic interaction that reduces the 14 reactivity of acylated proline residues at the C-terminus of peptides. 15 Here, we harness the enhanced reactivity of prolyl selenoesters and a 16 trans-γ-selenoproline moiety to access the elusive proline−proline 17 junction for the first time through a diselenide−selenoester ligation− 18 deselenization manifold. The efficient nature of this chemistry is 19 highlighted in the high-yielding one-pot assembly of two proline-rich 20 polypeptide targets, submaxillary gland androgen regulated protein 3B 21 and lumbricin-1. This method provides access to the most challenging of ligation junctions, thus enabling the construction of 22 previously intractable peptide and protein targets of increasing structural complexity