Regular Incidence Complexes, Polytopes, and C-Groups

Regular incidence complexes are combinatorial incidence structures generalizing regular convex polytopes, regular complex polytopes, various types of incidence geometries, and many other highly symmetric objects. The special case of abstract regular polytopes has been well-studied. The paper describes the combinatorial structure of a regular incidence complex in terms of a system of distinguished generating subgroups of its automorphism group or a flag-transitive subgroup. Then the groups admitting a flag-transitive action on an incidence complex are characterized as generalized string C-groups. Further, extensions of regular incidence complexes are studied, and certain incidence complexes particularly close to abstract polytopes, called abstract polytope complexes, are investigated.Comment: 24 pages; to appear in "Discrete Geometry and Symmetry", M. Conder, A. Deza, and A. Ivic Weiss (eds), Springe

Preferential substrate use decreases priming effects in contrasting treeline soils

This is the final version. Available on open access from Springer via the DOI in this recordData availability: All data generated during the current study are presented in the manuscript and available from the authors.Climate change currently manifests in upward and northward shifting treelines, which encompasses changes to the carbon (C) and nitrogen (N) composition of organic inputs to soils. Whether these changed inputs will increase or decrease microbial mineralisation of native soil organic matter remains unknown, making it difficult to estimate how treeline shifts will affect the C balance. Aiming to improve mechanistic understanding of C cycling in regions experiencing treeline shifts, we quantified priming effects in soils of high altitudes (Peruvian Andes) and high latitudes (subarctic Sweden), differentiating landcover types (boreal forest, tropical forest, tundra heath, Puna grassland) and soil horizons (organic, mineral). In a controlled laboratory incubation, soils were amended with substrates of different C:N, composed of an organic C source at a constant ratio of 30% substrate-C to microbial biomass C, combined with different levels of a nutrient solution neutral in pH. Substrate additions elicited both positive and negative priming effects in both ecosystems, independent from substrate C:N. Positive priming prevailed above the treeline in high altitudes and in mineral soils in high latitudes, where consequently climate change-induced treeline shifts and deeper rooting plants may enhance SOM-mineralisation and soil C emissions. However, such C loss may be compensated by negative priming, which dominated in the other soil types and was of larger magnitude than positive priming. In line with other studies, these results indicate a consistent mechanism linking decreased SOM-mineralisation (negative priming) to increased microbial substrate utilisation, suggesting preferential substrate use as a potential tool to support soil C storage. Graphical abstract: [Figure not available: see fulltext.]Natural Environment Research Council (NERC

Assessment of H2_{2}S in vivo using the newly developed mitochondria-targeted mass spectrometry probe MitoA

Hydrogen sulfide (H$_{2}$S) is produced endogenously in vivo and has multiple effects on signaling pathways and cell function. Mitochondria can be both an H$_{2}$S source and sink, and many of the biological effects of H$_{2}$S relate to its interactions with mitochondria. However, the significance of mitochondrial H$_{2}$S is uncertain, in part due to the difficulty of assessing changes in its concentration in vivo Although a number of fluorescent H$_{2}$S probes have been developed these are best suited to cells in culture and cannot be used in vivo To address this unmet need we have developed a mitochondria-targeted H$_{2}$S probe, MitoA, which can be used to assess relative changes in mitochondrial H$_{2}$S levels in vivo MitoA comprises a lipophilic triphenylphosphonium (TPP) cation coupled to an aryl azide. The TPP cation leads to the accumulation of MitoA inside mitochondria within tissues in vivo There, the aryl azido group reacts with H$_{2}$S to form an aryl amine (MitoN). The extent of conversion of MitoA to MitoN thus gives an indication of the levels of mitochondrial H$_{2}$S in vivo Both compounds can be detected sensitively by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the tissues, and quantified relative to deuterated internal standards. Here we describe the synthesis and characterization of MitoA and show that it can be used to assess changes in mitochondrial H$_{2}$S levels in vivo As a proof of principle we used MitoA to show that H$_{2}$S levels increase in vivo during myocardial ischemia.This work was supported in part by Medical Research Council UK Grant MC_U105663142, Wellcome Trust Investigator award 110159/Z/15/Z (to M. P. M.), Biotechnology and Biological Sciences Research Council Grant BB/I012826/1, Wellcome Trust Investigator award 110158/Z/15/Z (to R. C. H.), and a Consejo Nacional de Ciencia y Technología studentship (to C. B.-G.)

An investigation on the presence of Chlamydiaceae in Swedish dogs

<p>Abstract</p> <p>Background</p> <p>Bacteria belonging to the family <it>Chlamydiaceae </it>cause a broad spectrum of diseases in a wide range of hosts, including man, other mammals, and birds. Upper respiratory and genital diseases are common clinical problems caused by <it>Chlamydiaceae</it>. Very little is known about chlamydial infections in dogs. Few clinical reports on natural disease in dogs describe mainly conjunctival and upper respiratory signs, and the role of <it>Chlamydiaceae </it>in genital disease is unclear. The present study aimed at studying the prevalence of <it>Chlamydiaceae </it>in healthy dogs and in dogs with genital or upper respiratory disease, including conjunctivitis.</p> <p>Methods</p> <p>A real-time polymerase chain reaction (PCR) for <it>Chlamydiaceae </it>was used to detect any chlamydial species within this family. Swab samples from the conjunctiva and the mucosal membranes of the oropharynx, rectum and genital tract were taken from 79 dogs: 27 clinically healthy dogs, 25 dogs with clinical signs from the genital tract and 28 dogs with conjunctivitis. There were 52 female and 27 male dogs. From 7 of the male dogs, additional semen samples were analysed.</p> <p>Results</p> <p>No <it>Chlamydiaceae </it>were detected from any dog.</p> <p>Conclusions</p> <p>Although the number of dogs that was included is limited, the results suggest that cases of <it>Chlamydiaceae </it>in dogs probably are related to infection from other species, and that dogs in general do not harbour <it>Chlamydiaceae</it>. Bacteria belonging to the family <it>Chlamydiaceae </it>do not seem to be of major importance for genital or ocular disease in Swedish dogs.</p

Thiothymidine combined with UVA as a potential novel therapy for bladder cancer

BACKGROUND: Thiothymidine (S4TdR) can be incorporated into DNA and sensitise cells to DNA damage and cell death following exposure to UVA light. Studies were performed to determine if the combination of S4TdR and UVA could be an effective treatmentfor bladder cancer. METHODS: Uptake and incorporation of S4TdR was determined in rat and human bladder tumour cell lines. Measures of DNA crosslinking and apoptosis were also performed. In vivo activity of the combination of S4TdR and UVA was investigated in an orthotopic model of bladder cancer in rats. RESULTS: Thiothymidine (200 uM) replaced up to 0.63% of thymidine in rat and tumour bladder cancer cells. The combination of S4TdR (10–200 uM) and UVA (1–5 kJm-2) caused apoptosis and cell death at doses that were not toxic alone. Addition of raltitrexed (Astra Zeneca, Alderley Edge, Cheshire, UK) increased the incorporation of S4TdR into DNA (up to 20-fold at IC5) and further sensitised cells to UVA. Cytotoxic effect was associated with crosslinking of DNA, at least partially to protein. Intravenous administration of S4TdR, in combination with UVA delivered directly to the bladder, resulted in an antitumour effect in three of five animals treated. CONCLUSION: These data indicate that the combination of S4TdR and UVA has potential as a treatment for bladder cancer, and give some insight into the mechanism of action. Further work is necessary to optimise the delivery of the two components

Processing DNA molecules as text

Polymerase Chain Reaction (PCR) is the DNA-equivalent of Gutenberg’s movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting, both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Biology labs engage daily in DNA processing—the creation of variations and combinations of existing DNA—using a plethora of manual labor-intensive methods such as site-directed mutagenesis, error-prone PCR, assembly PCR, overlap extension PCR, cleavage and ligation, homologous recombination, and others. So far no universal method for DNA processing has been proposed and, consequently, no engineering discipline that could eliminate this manual labor has emerged. Here we present a novel operation on DNA molecules, called Y, which joins two DNA fragments into one, and show that it provides a foundation for DNA processing as it can implement all basic text processing operations on DNA molecules including insert, delete, replace, cut and paste and copy and paste. In addition, complicated DNA processing tasks such as the creation of libraries of DNA variants, chimeras and extensions can be accomplished with DNA processing plans consisting of multiple Y operations, which can be executed automatically under computer control. The resulting DNA processing system, which incorporates our earlier work on recursive DNA composition and error correction, is the first demonstration of a unified approach to DNA synthesis, editing, and library construction

Investigating Agrobacterium-Mediated Transformation of Verticillium albo-atrum on Plant Surfaces

Background: Agrobacterium tumefaciens has long been known to transform plant tissue in nature as part of its infection process. This natural mechanism has been utilised over the last few decades in laboratories world wide to genetically manipulate many species of plants. More recently this technology has been successfully applied to non-plant organisms in the laboratory, including fungi, where the plant wound hormone acetosyringone, an inducer of transformation, is supplied exogenously. In the natural environment it is possible that Agrobacterium and fungi may encounter each other at plant wound sites, where acetosyringone would be present, raising the possibility of natural gene transfer from bacterium to fungus. Methodology/Principal Findings: We investigate this hypothesis through the development of experiments designed to replicate such a situation at a plant wound site. A. tumefaciens harbouring the plasmid pCAMDsRed was co-cultivated with the common plant pathogenic fungus Verticillium albo-atrum on a range of wounded plant tissues. Fungal transformants were obtained from co-cultivation on a range of plant tissue types, demonstrating that plant tissue provides sufficient vir gene inducers to allow A. tumefaciens to transform fungi in planta. Conclusions/Significance: This work raises interesting questions about whether A. tumefaciens may be able to transform organisms other than plants in nature, or indeed should be considered during GM risk assessments, with furthe