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"J. Wilson"
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The architecture of the Gram-positive bacterial cell wall
The primary structural component of the bacterial cell wall is peptidoglycan, which is essential for viability and the synthesis of which is the target for crucial antibiotics
1
,
2
. Peptidoglycan is a single macromolecule made of glycan chains crosslinked by peptide side branches that surrounds the cell, acting as a constraint to internal turgor
1
,
3
. In Gram-positive bacteria, peptidoglycan is tens of nanometres thick, generally portrayed as a homogeneous structure that provides mechanical strength
4
–
6
. Here we applied atomic force microscopy
7
–
12
to interrogate the morphologically distinct
Staphylococcus aureus
and
Bacillus subtilis
species, using live cells and purified peptidoglycan. The mature surface of live cells is characterized by a landscape of large (up to 60 nm in diameter), deep (up to 23 nm) pores constituting a disordered gel of peptidoglycan. The inner peptidoglycan surface, consisting of more nascent material, is much denser, with glycan strand spacing typically less than 7 nm. The inner surface architecture is location dependent; the cylinder of
B. subtilis
has dense circumferential orientation, while in
S. aureus
and division septa for both species, peptidoglycan is dense but randomly oriented. Revealing the molecular architecture of the cell envelope frames our understanding of its mechanical properties and role as the environmental interface
13
,
14
, providing information complementary to traditional structural biology approaches.
Using high-resolution atomic force microscopy of live cells, the authors present an updated view of the cell walls of both
Staphylococcus aureus
and
Bacillus subtilis
.
Journal Article
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/.
Journal Article
A history of optical telescopes in astronomy
\"This book is uniquely about the relationship between the optical telescope and astronomy as they developed together. It covers the time between the telescope's pivotal invention in the 1600's up to the modern era of space-based telescopes. Over the intervening centuries, there were huge improvements in the optical resolution of telescopes, along with changes in their positioning and nature of application that forever altered the course of astronomy. For a long time, the field was an exclusive club for self-motivated stargazers who could afford to build their own telescopes. Many of these leisure-time scholars left their mark by virtue of their meticulous observations and record keeping. Although they would now be considered amateurs, these figures and their contributions were pivotal and are covered in this book alongside professionals, for the first time giving a complete picture of the history of telescopic science.\"--Back cover.
Book
DNA metabarcoding of insects and allies: an evaluation of primers and pipelines
Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80–90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.
Journal Article
The growth of the firm: An attention-based view
Research Summary: Although most theories of growth presume that growth varies with the focus and limits of managerial attention, the actual role played by attention has remained largely implicit. In contrast, this article explicitly considers attention structure and the processes that place sustained focus on growth issues. We explain how attention structure—specialized attention within a particular unit and integrated attention between units—affects both bottom-up (stimulus-driven) and top-down (schema-driven) attentional processing of new issues. We also examine the relationship between attention structure and divisional interdependencies, identifying conditions under which different attentional patterns generate organizational tensions that lead to architectural elaboration: the delineation of new organizational units. This logic is illustrated with examples from Motorola, a large telecommunications equipment provider, during a period of sustained growth. In linking theories of growth with the attention-based view (ABV), we augment both perspectives and offer an approach that provides a better understand growth's cognitive underpinnings. Managerial Summary: We examine how, within a multidivisional firm, the pattern of organizational attention affects firm growth. We highlight the attention focus within and between divisions and the corporate office and specific processes that shape the intensity and direction of attention in the firm's constituent units. In particular, we examine how corporate interventions, appointment of managerial resources, prototyping, and corporate charters direct managerial attention and the identification and advancement new opportunities in support of growth. Our approach also considers how attention patterns and formal organizational structure interact to cause tensions between managers, and when these tensions lead to the delineation of new subunits. To illustrate our logic, we use examples drawn from Motorola, a large telecommunications equipment provider, during a period of sustained growth. Our approach offers managers insights into attentional design of the multidivisional firm.
Journal Article
Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses
The host innate immune response mediated by type I interferon (IFN) and the resulting up-regulation of hundreds of interferon-stimulated genes (ISGs) provide an immediate barrier to virus infection. Studies of the type I 'interferome' have mainly been carried out at a single species level, often lacking the power necessary to understand key evolutionary features of this pathway. Here, using a single experimental platform, we determined the properties of the interferomes of multiple vertebrate species and developed a webserver to mine the dataset. This approach revealed a conserved 'core' of 62 ISGs, including genes not previously associated with IFN, underscoring the ancestral functions associated with this antiviral host response. We show that gene expansion contributes to the evolution of the IFN system and that interferomes are shaped by lineage-specific pressures. Consequently, each mammal possesses a unique repertoire of ISGs, including genes common to all mammals and others unique to their specific species or phylogenetic lineages. An analysis of genes commonly down-regulated by IFN suggests that epigenetic regulation of transcription is a fundamental aspect of the IFN response. Our study provides a resource for the scientific community highlighting key paradigms of the type I IFN response.
Journal Article