High quality genome annotation and expression visualisation of a mupirocin-producing bacterium.

Pseudomonas strain NCIMB10586, in the P. fluorescens subgroup, produces the polyketide antibiotic mupirocin, and has potential as a host for industrial production of a range of valuable products. To underpin further studies on its genetics and physiology, we have used a combination of standard and atypical approaches to achieve a quality of the genome sequence and annotation, above current standards for automated pathways. Assembly of Illumina reads to a PacBio genome sequence created a retrospectively hybrid assembly, identifying and fixing 415 sequencing errors which would otherwise affect almost 5% of annotated coding regions. Our annotation pipeline combined automation based on related well-annotated genomes and stringent, partially manual, tests for functional features. The strain was close to P. synxantha and P. libaniensis and was found to be highly similar to a strain being developed as a weed-pest control agent in Canada. Since mupirocin is a secondary metabolite whose production is switched on late in exponential phase, we carried out RNAseq analysis over an 18 h growth period and have developed a method to normalise RNAseq samples as a group, rather than pair-wise. To review such data we have developed an easily interpreted way to present the expression profiles across a region, or the whole genome at a glance. At the 2-hour granularity of our time-course, the mupirocin cluster increases in expression as an essentially uniform bloc, although the mupirocin resistance gene stands out as being expressed at all the time points.

The missing N1 or jittered P2: Electrophysiological correlates of pattern glare in the time and frequency domain.

Excessive sensitivity to certain visual stimuli (cortical hyperexcitability) is associated with a number of neurological disorders including migraine, epilepsy, multiple sclerosis, autism and possibly dyslexia. Others show disruptive sensitivity to visual stimuli with no other obvious pathology or symptom profile (visual stress) which can extend to discomfort and nausea. We used event-related potentials (ERPs) to explore the neural correlates of visual stress and headache proneness. We analysed ERPs in response to thick (0.37 cycles per degree [c/deg]), medium (3 c/deg) and thin (12 c/deg) gratings, using mass univariate analysis, considering three factors in the general population: headache proneness, visual stress and discomfort. We found relationships between ERP features and the headache and discomfort factors. Stimulus main effects were driven by the medium stimulus regardless of participant characteristics. Participants with high discomfort ratings had larger P1 components for the initial presentation of medium stimuli, suggesting initial cortical hyperexcitability that is later suppressed. The participants with high headache ratings showed atypical N1-P2 components for medium stripes relative to the other stimuli. This effect was present only after repeated stimulus presentation. These effects were also explored in the frequency domain, suggesting variations in intertrial theta band phase coherence. Our results suggest that discomfort and headache in response to striped stimuli are related to different neural processes; however, more exploration is needed to determine whether the results translate to a clinical migraine population.

Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR.

Plasmids are potent vehicles for spread of antibiotic resistance genes in bacterial populations and often persist in the absence of selection due to efficient maintenance mechanisms. We previously constructed non-conjugative high copy number plasmid vectors that efficiently displace stable plasmids from enteric bacteria in a laboratory context by blocking their replication and neutralising their addiction systems. Here we assess a low copy number broad-host-range self-transmissible IncP-1 plasmid as a vector for such curing cassettes to displace IncF and IncK plasmids. The wild type plasmid carrying the curing cassette displaces target plasmids poorly but derivatives with deletions near the IncP-1 replication origin that elevate copy number about two-fold are efficient. Verification of this in mini IncP-1 plasmids showed that elevated copy number was not sufficient and that the parB gene, korB, that is central to its partitioning and gene control system, also needs to be included. The resulting vector can displace target plasmids from a laboratory population without selection and demonstrated activity in a mouse model although spread is less efficient and requires additional selection pressure.

Defining the genes for the final steps in biosynthesis of the complex polyketide antibiotic mupirocin by Pseudomonas fluorescens NCIMB10586.

The mupirocin trans-AT polyketide synthase pathway, provides a model system for manipulation of antibiotic biosynthesis. Its final phase involves removal of the tertiary hydroxyl group from pseudomonic acid B, PA-B, producing the fully active PA-A in a complex series of steps. To further clarify requirements for this conversion, we fed extracts containing PA-B to mutants of the producer strain singly deficient in each mup gene. This additionally identified mupM and mupN as required plus the sequence but not enzymic activity of mupL and ruled out need for other mup genes. A plasmid expressing mupLMNOPVCFU + macpE together with a derivative of the producer P. fluorescens strain NCIMB10586 lacking the mup cluster allowed conversion of PA-B to PA-A. MupN converts apo-mAcpE to holo-form while MupM is a mupirocin-resistant isoleucyl tRNA synthase, preventing self-poisoning. Surprisingly, the expression plasmid failed to allow the closely related P. fluorescens strain SBW25 to convert PA-B to PA-A.

Atomistic Approach toward Selective Photocatalytic Oxidation of a Mustard-Gas Simulant: A Case Study with Heavy-Chalcogen-Containing PCN-57 Analogues.

Here we describe the synthesis of two Zr-based benzothiadiazole- and benzoselenadiazole-containing metal-organic frameworks (MOFs) for the selective photocatalytic oxidation of the mustard gas simulant, 2-chloroethyl ethyl sulfide (CEES). The photophysical properties of the linkers and MOFs are characterized by steady-state absorption and emission, time-resolved emission, and ultrafast transient absorption spectroscopy. The benzoselenadiazole-containing MOF shows superior catalytic activity compared to that containing benzothiadiazole with a half-life of 3.5 min for CEES oxidation to nontoxic 2-chloroethyl ethyl sulfoxide (CEESO). Transient absorption spectroscopy performed on the benzoselenadiazole linker reveals the presence of a triplet excited state, which decays with a lifetime of 9.4 µs, resulting in the generation of singlet oxygen for photocatalysis. This study demonstrates the effect of heavy chalcogen substitution within a porous framework for the modulation of photocatalytic activity.

Direct Observation of a Charge-Transfer State Preceding High-Yield Singlet Fission in Terrylenediimide Thin Films.

Singlet exciton fission (SF) in organic chromophore assemblies results in the conversion of one singlet exciton (S1) into two triplet excitons (T1), provided that the overall process is exoergic, i.e., E(S1) > 2E(T1). We report on SF in thin polycrystalline films of two terrylene-3,4:11,12-bis(dicarboximide) (TDI) derivatives 1 and 2, which crystallize into two distinct π-stacked structures. Femtosecond transient absorption spectroscopy (fsTA) reveals a charge-transfer state preceding a 190% T1 yield in films of 1, where the π-stacked TDI molecules are rotated by 23° along an axis perpendicular to their π systems. In contrast, when the TDI molecules are slip-stacked along their N-N axes in films of 2, fsTA shows excimer formation, followed by a 50% T1 yield.

Enabling singlet fission by controlling intramolecular charge transfer in π-stacked covalent terrylenediimide dimers.

When an assembly of two or more molecules absorbs a photon to form a singlet exciton, and the energetics and intermolecular interactions are favourable, the singlet exciton can rapidly and spontaneously produce two triplet excitons by singlet fission. To understand this process is important because it may prove to be technologically significant for enhancing solar-cell performance. Theory strongly suggests that charge-transfer states are involved in singlet fission, but their role has remained an intriguing puzzle and, up until now, no molecular system has provided clear evidence for such a state. Here we describe a terrylenediimide dimer that forms a charge-transfer state in a few picoseconds in polar solvents, and undergoes equally rapid, high-yield singlet fission in nonpolar solvents. These results show that adjusting the charge-transfer-state energy relative to those of the exciton states can serve to either inhibit or promote singlet fission.

Singlet Fission via an Excimer-Like Intermediate in 3,6-Bis(thiophen-2-yl)diketopyrrolopyrrole Derivatives.

Singlet fission (SF) in polycrystalline thin films of four 3,6-bis(thiophen-2-yl)diketopyrrolopyrrole (TDPP) chromophores with methyl (Me), n-hexyl (C6), triethylene glycol (TEG), and 2-ethylhexyl (EH) substituents at the 2,5-positions is found to involve an intermediate excimer-like state. The four different substituents yield four distinct intermolecular packing geometries, resulting in variable intermolecular charge transfer (CT) interactions in the solid. SF from the excimer state of Me, C6, TEG, and EH takes place in τSF = 22, 336, 195, and 1200 ps, respectively, to give triplet yields of 200%, 110%, 110%, and 70%, respectively. The transient spectra of the excimer-like state and its energetic proximity to the lowest excited singlet state in these derivatives suggests that this state may be the multiexciton (1)(T1T1) state that precedes formation of the uncorrelated triplet excitons. The excimer decay rates correlate well with the SF efficiencies and the degree of intermolecular donor-acceptor interactions resulting from π-stacking of the thiophene donor of one molecule with the DPP core acceptor in another molecule as observed in the crystal structures. Such interactions are found to also increase with the SF coupling energies, as calculated for each derivative. These structural and spectroscopic studies afford a better understanding of the electronic interactions that enhance SF in chromophores having strong intra- and intermolecular CT character.

Electrophysiological measurement of the effect of inter-stimulus competition on early cortical stages of human vision.

Competition between inputs in early visual cortex has been established as a key determinant in perception through decades of animal single cell and human fMRI research. We developed a novel ERP paradigm allowing this competition to be studied in humans, affording an opportunity to gain further insight into how competition is reflected at the neural level. Checkerboard stimuli were presented to elicit C1 (indexing processing in V1), C2 (hypothesized to reflect V1 after extrastriate feedback), and P1 (extrastriate) components. Stimuli were presented in three randomized conditions: single stimulus, near proximity pairs and far proximity pairs. Importantly, near stimuli (0.16° visual angle apart) were positioned to compete in primary visual cortex, whereas far stimuli (2° apart) were positioned to compete in extrastriate visual areas. As predicted, the degree and spatial range of competition increased from the C1 component to the C2 and P1 components. Specifically, competitive interactions in C1 amplitude were modest and present only for near-proximity pairs, whereas substantial competition was present for the P1, even for far-proximity pairs. To our knowledge, this is the first study to measure how competition unfolds over time in human visual cortex. Importantly, this method provides an empirical means of measuring competitive interactions at specific stages of visual processing, rendering it possible to rigorously test predictions about the effects of competition on perception, attention, and working memory.

Neural Mechanisms Underlying Visual Short-Term Memory Gain for Temporally Distinct Objects.

Recent research has shown that visual short-term memory (VSTM) can substantially be improved when the to-be-remembered objects are split in 2 half-arrays (i.e., sequenced) or the entire array is shown twice (i.e., repeated), rather than presented simultaneously. Here we investigate the hypothesis that sequencing and repeating displays overcomes attentional "bottlenecks" during simultaneous encoding. Using functional magnetic resonance imaging, we show that sequencing and repeating displays increased brain activation in extrastriate and primary visual areas, relative to simultaneous displays (Study 1). Passively viewing identical stimuli did not increase visual activation (Study 2), ruling out a physical confound. Importantly, areas of the frontoparietal attention network showed increased activation in repetition but not in sequential trials. This dissociation suggests that repeating a display increases attentional control by allowing attention to be reallocated in a second encoding episode. In contrast, sequencing the array poses fewer demands on control, with competition from nonattended objects being reduced by the half-arrays. This idea was corroborated by a third study in which we found optimal VSTM for sequential displays minimizing attentional demands. Importantly these results provide support within the same experimental paradigm for the role of stimulus-driven and top-down attentional control aspects of biased competition theory in setting constraints on VSTM.

The role of biased competition in visual short-term memory.

Despite being extensively studied, many important questions regarding visual short-term memory (VSTM) are yet to be fully answered. The present review seeks to explore the extent to which competitive interactions present during perception of stimuli may also operate during stimulus encoding and/or maintenance in VSTM. Additionally, the paper provides an overview of the methods and approaches that have been used to study the properties of VSTM, and a review of research into the limits of VSTM capacity. We take as our starting point the biased competition model of attention (Desimone & Duncan, 1995) and discuss the influence that such competition may have on the limited capacity of VSTM by a review of the literature and by recent experiments from Shapiro's lab. The present report outlines several experiments that provide results consistent with the idea that low-level competitive interactions may influence VSTM, with the aim of stimulating further research into this new area.

Pumping iron: mechanisms for iron uptake by Campylobacter.

Campylobacter requires iron for successful colonization of the host. In the last 7 years, a wealth of data has been generated allowing detailed molecular characterization of Campylobacter iron-uptake systems. Several exogenous siderophores have been identified as sources of ferric iron for Campylobacter. Ferri-enterochelin uptake requires both the outer-membrane receptor protein CfrA and the inner-membrane ABC transporter system CeuBCDE. Ferrichrome has been shown to support growth of some Campylobacter jejuni strains and the presence of homologues of Escherichia coli fhuABD genes was proposed; the Cj1658-Cj1663 system appears to be involved in the uptake of ferri-rhodotorulic acid. In addition to siderophores, the importance of host iron sources was highlighted by recent studies demonstrating that C. jejuni can exploit haem compounds and the transferrins using ChuABCDZ and Cj0173c-Cj0178, respectively. An additional putative receptor, Cj0444, present in some, but not all, strains has not yet been characterized. Following diffusion through the outer membrane, inner-membrane transport of ferrous iron can occur via the FeoB protein. While it may be assumed that all systems are not essential, there is growing evidence supporting the need for multiple iron-uptake systems for successful host colonization by Campylobacter. In light of this, comparative molecular characterization of iron systems in all Campylobacter strains is necessary to gain further insight into the pathogenesis of members of this genus.

Utilization of lactoferrin-bound and transferrin-bound iron by Campylobacter jejuni.

Campylobacter jejuni NCTC 11168 was capable of growth to levels comparable with FeSO4 in defined iron-limited medium (minimal essential medium alpha [MEMalpha]) containing ferrilactoferrin, ferritransferrin, or ferri-ovotransferrin. Iron was internalized in a contact-dependent manner, with 94% of cell-associated radioactivity from either 55Fe-loaded transferrin or lactoferrin associated with the soluble cell fraction. Partitioning the iron source away from bacteria significantly decreased cellular growth. Excess cold transferrin or lactoferrin in cultures containing 55Fe-loaded transferrin or lactoferrin resulted in reduced levels of 55Fe uptake. Growth of C. jejuni in the presence of ferri- and an excess of apoprotein reduced overall levels of growth. Following incubation of cells in the presence of ferrilactoferrin, lactoferrin became associated with the cell surface; binding levels were higher after growth under iron limitation. A strain carrying a mutation in the cj0178 gene from the iron uptake system Cj0173c-Cj0178 demonstrated significantly reduced growth promotion in the presence of ferrilactoferrin in MEMalpha compared to wild type but was not affected in the presence of heme. Moreover, this mutant acquired less 55Fe than wild type when incubated with 55Fe-loaded protein and bound less lactoferrin. Complementation restored the wild-type phenotype when cells were grown with ferrilactoferrin. A mutant in the ABC transporter system permease gene (cj0174c) showed a small but significant growth reduction. The cj0176c-cj0177 intergenic region contains two separate Fur-regulated iron-repressible promoters. This is the first demonstration that C. jejuni is capable of acquiring iron from members of the transferrin protein family, and our data indicate a role for Cj0178 in this process.