ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data

Background

Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, directly from paired-end short read data.

Results

ISMapper was validated using three types of short read data: (i) simulated reads from a variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences were available for comparison, and (iii) Illumina reads from 7 Acinetobacter baumannii isolates for which predicted IS locations were tested using PCR. A total of 20 genomes, including 13 species and 32 distinct IS, were used for validation. ISMapper correctly identified 97 % of known IS insertions in the analysis of simulated reads, and 98 % in real Illumina reads. Subsampling of real Illumina reads to lower depths indicated ISMapper was able to correctly detect insertions for average genome-wide read depths >20x, although read depths >50x were required to obtain confident calls that were highly-supported by evidence from reads. All ISAba1 insertions identified by ISMapper in the A. baumannii genomes were confirmed by PCR. In each A. baumannii genome, ISMapper successfully identified an IS insertion upstream of the ampC beta-lactamase that could explain phenotypic resistance to third-generation cephalosporins. The utility of ISMapper was further demonstrated by profiling genome-wide IS6110 insertions in 138 publicly available Mycobacterium tuberculosis genomes, revealing lineage-specific insertions and multiple insertion hotspots.

Conclusions

ISMapper provides a rapid and robust method for identifying IS insertion sites directly from short read data, with a high degree of accuracy demonstrated across a wide range of bacteria.     

Pirfenidone inhibits TGF-beta expression in malignant glioma cells

Due to its immunosuppressive properties, the cytokine transforming growth factor (TGF)-beta has become a promising target in the experimental treatment of human malignant gliomas. Here, we report that the antifibrotic drug 5-methyl-1-phenyl-2-(1H)-pyridone (pirfenidone, PFD) elicits growth-inhibitory effects and reduces TGF-beta2 protein levels in human glioma cell lines. This reduction in TGF-beta2 is biologically relevant since PFD treatment reduces the growth inhibition of TGF-beta-sensitive CCL-64 cells mediated by conditioned media of glioma cells. The downregulation of TGF-beta is mediated at multiple levels. PFD leads to a reduction of TGF-beta2 mRNA levels and of the mature TGF-beta2 protein due to decreased expression and direct inhibition of the TGF-beta pro-protein convertase furin. In addition, PFD reduces the protein levels of the matrix metalloproteinase (MMP)-11, a TGF-beta target gene and furin substrate involved in carcinogenesis. These data define PFD or PFD-related agents as promising agents for human cancers associated with enhanced TGF-beta activity.     

Micronized Copper Wood Preservatives: Efficacy of Ion,Nano, and Bulk Copper against the Brown Rot Fungus Rhodonia placenta

Recently introduced micronized copper (MC) formulations, consisting of a nanosized fraction of basic copper (Cu) carbonate (CuCO₃·Cu(OH)₂) nanoparticles (NPs), were introduced to the market for wood protection. Cu NPs may presumably be more effective against wood-destroying fungi than bulk or ionic Cu compounds. In particular, Cu- tolerant wood-destroying fungi may not recognize NPs, which may penetrate into fungal cell walls and membranes and exert their impact. The objective of this study was to assess if MC wood preservative formulations have a superior efficacy against Cu-tolerant wood-destroying fungi due to nano effects than conventional Cu biocides. After screening a range of wood-destroying fungi for their resistance to Cu, we investigated fungal growth of the Cu-tolerant fungus Rhodonia placenta in solid and liquid media and on wood treated with MC azole (MCA). In liquid cultures we evaluated the fungal response to ion, nano and bulk Cu distinguishing the ionic and particle effects by means of the Cu²⁺ chelator ammonium tetrathiomolybdate (TTM) and measuring fungal biomass, oxalic acid production and laccase activity of R. placenta. Our results do not support the presence of particular nano effects of MCA against R. placenta that would account for an increased antifungal efficacy, but provide evidence that attribute the main effectiveness of MCA to azoles.     

Influence of human impact and bedrock differences on the vegetational history of the Insubrian Southern Alps

Vegetation history for the study region is reconstructed on the basis of pollen, charcoal and AMS¹⁴C investigations of lake sediments from Lago del Segrino (calcareous bedrock) and Lago di Muzzano (siliceous bedrock). Late-glacial forests were characterised byBetula andPinus sylvestris. At the beginning of the Holocene they were replaced by temperate continental forest and shrub communities. A special type of temperate lowland forest, withAbies alba as the most important tree, was present in the period 8300 to 4500 B.P. Subsequently,Fagus, Quercus andAlnus glutinosa were the main forest components andA. alba ceased to be of importance.Castanea sativa andJuglans regia were probably introduced after forest clearance by fire during the first century A.D. On soils derived from siliceous bedrock,C. sativa was already dominant at ca. A.D. 200 (A.D. dates are in calendar years). In limestone areas, however,C. sativa failed to achieve a dominant role. After the introduction ofC. sativa, the main trees were initially oak (Quercus spp.) and later the walnut (Juglans regia). Ostrya carpinifolia became the dominant tree around Lago del Segrino only in the last 100–200 years though it had spread into the area at ca. 5000 cal. B.C. This recent expansion ofOstrya is confirmed at other sites and appears to be controlled by human disturbances involving especially clearance. It is argued that these forests should not be regarded as climax communities. It is suggested that under undisturbed succession they would develop into mixed deciduous forests consisting ofFraxinus excelsior, Tilia, Ulmus, Quercus andAcer.     

Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system

Nonmotile microorganisms often enter new habitats by co-transport with motile microorganisms. Here, we report that also lytic phages can co-transport with hyphal-riding bacteria and facilitate bacterial colonization of a new habitat. This is comparable to the concept of biological invasions in macroecology. In analogy to invasion frameworks in plant and animal ecology, we tailored spatially organized, water-unsaturated model microcosms using hyphae of Pythium ultimum as invasion paths and flagellated soil-bacterium Pseudomonas putida KT2440 as carrier for co-transport of Escherichia virus T4. P. putida KT2440 efficiently dispersed along P. ultimum to new habitats and dispatched T4 phages across air gaps transporting ≈0.6 phages bacteria⁻¹. No T4 displacement along hyphae was observed in the absence of carrier bacteria. If E. coli occupied the new habitat, T4 co-transport fueled the fitness of invading P. putida KT2440, while the absence of phage co-transport led to poor colonization followed by extinction. Our data emphasize the importance of hyphal transport of bacteria and associated phages in regulating fitness and composition of microbial populations in water-unsaturated systems. As such co-transport seems analogous to macroecological invasion processes, hyphosphere systems with motile bacteria and co-transported phages could be useful models for testing hypotheses in invasion ecology.Subject terms: Microbial ecology, Ecosystem ecology, Macroecology, Population dynamics     

Cephaloglycin and Its Biologically Active Metabolite Desacetylcephaloglycin

Chromatographic studies and microbiological assays show that, after oral administration, cephaloglycin is partially converted in man to a biologically active metabolite desacetylcephaloglycin. The antibacterial activity of this metabolite compared to that of cephaloglycin is equivalent against gram-positive organisms but is lower against gram-negative bacilli. Successful therapy of urinary tract infections with cephaloglycin must be mainly attributed to the antibacterial activity of this metabolite. At the present time, it is not possible to assess what influence low amounts of unaltered cephaloglycin have on the outcome of therapy.     

Sex steroid and glucocorticoid receptors in the bursa of Fabricius of obese strain chickens spontaneously developing autoimmune thyroiditis

The female sex develops autoimmune disease far more often than the male. This is claimed to be due to differences in peripheral sex steroid levels. We have examined in the bursa of Fabricius of Obese strain (OS) chickens, which spontaneously develop autoimmune thyroiditis, as well as in their healthy counterparts androgen(AR)-, estrogen(ER)-, progestin(PR)- and glucocorticoid(GR)-receptors in an attempt to elucidate possible further pathomechanisms, namely at the target site of steroid hormones. The characterization (affinity, specificity, association- and dissociation-rate, sedimentation behaviour) of all four types of receptors revealed no difference between sex or strain. Furthermore, the ontogeny study of the receptor capacity and affinity from the 7th embryonic day (i.e. before lymphocyte settlement) until bursa involution, again showed no difference between OS and healthy chickens of either sex. Thus, it can be concluded that the principal sex dependency of the susceptibility to autoimmune disease results predominantly from differences in sex steroid levels per se, although alterations in mechanisms beyond the cytosolic receptor level can presently not be excluded.     

Incidence of leukaemia and other malignant diseases following injections of the short-lived α-emitter <Superscript>224</Superscript>Ra into man

We performed an epidemiological study on 1,471 ankylosing spondylitis patients treated with repeated intravenous injections of the short lived α-emitter ²²⁴Ra (excluding radiation therapy with X-rays) between 1948 and 1975. These patients have been followed together with a control group of 1,324 ankylosing spondylitis patients treated neither with radioactive drugs nor with X-rays. The mean follow-up time was 26.3 years in the exposed and 24.6 years in the control group. To date, causes of death have been ascertained for 1,006 exposed patients and 1,072 controls. Special emphasis was placed on the reporting of malignant diseases. Expected numbers of cases were computed for the age, sex and calendar year distribution of both groups using cancer registry incidence rates. In the exposed group 18 cases of kidney cancer (vs. 9.1 cases expected, P < 0.01) and 4 malignant thyroid tumours (vs. 1.2 cases expected, P = 0.03) were observed. In the control group the observed cases for these tumours were not significantly elevated. The most striking observation, however, were the 21 cases of leukaemia in the exposed group (vs. 6.8 cases expected, P < 0.001) compared to 12 cases of leukaemia in the control group (vs. 7.5 cases expected). Further sub-classification of the leukaemias demonstrated a high increase of myeloid leukaemia in the exposed group (12 cases observed vs. 2.9 cases expected, P < 0.001), and out of these, especially a high excess of acute myeloid leukaemias (7 cases observed vs. 1.8 expected, P = 0.003). In the controls the observed cases are within the expected range (4 myeloid leukaemias vs. 3.1 cases). This increase in total leukaemias as well as particularly in myeloid leukaemias is significant in direct comparison between the exposed and control groups too (P < 0.05). The enhanced leukaemia incidence in the exposed group is in line with the observation of increased leukaemia incidence in mice injected with ²²⁴Ra.