2,762 research outputs found
Chlamydia trachomatis: small genome, big challenges.
No full textChlamydial infections are highly newsworthy, but basic research into Chlamydia trachomatis is severely hampered by a series of formidable technical barriers. This has resulted in a paucity of information with respect to the genetics and population structure of these recalcitrant bacteria. Here we present a review of what is currently known about the genomics of C. trachomatis and discuss the usefulness of molecular typing systems and the prospects of developing a pan-chlamydial genome resourc
Dataset for Deep learning enabled design of complex transmission matrices for universal optical components
No full textData comprising Numerical simulation results and deep learning results to supprot article N. J. Dinsdale, P. R. Wiecha, M. Delaney, J. Reynolds, M. Ebert, I. Zeimpekis, D. J. Thomson, G. T. Reed, P. Lalanne, K. Vynck, O. L. Muskens "Deep learning enabled design of complex transmission matrices for universal optical components". ACS Photonics (2020). Each figure has a Readme file attached.</span
The nature and extent of plasmid variation in Chlamydia trachomatis
No full textChlamydia trachomatis is an obligate intracellular pathogen of humans, causing both the sexually transmitted infection, chlamydia, and the most common cause of infectious blindness, trachoma. The majority of sequenced C. trachomatis clinical isolates carry a 7.5-Kb plasmid, and it is becoming increasingly evident that this is a key determinant of pathogenicity. The discovery of the Swedish New Variant and the more recent Finnish variant highlight the importance of understanding the natural extent of variation in the plasmid. In this study we analysed 524 plasmid sequences from publicly available whole-genome sequence data. Single nucleotide polymorphisms (SNP) in each of the eight coding sequences (CDS) were identified and analysed. There were 224 base positions out of a total 7550 bp that carried a SNP, which equates to a SNP rate of 2.97%, nearly three times what was previously calculated. After normalising for CDS size, CDS8 had the highest SNP rate at 3.97% (i.e., number of SNPs per total number of nucleotides), whilst CDS6 had the lowest at 1.94%. CDS5 had the highest total number of SNPs across the 524 sequences analysed (2267 SNPs), whereas CDS6 had the least SNPs with only 85 SNPs. Calculation of the genetic distances identified CDS6 as the least variable gene at the nucleotide level (d = 0.001), and CDS5 as the most variable (d = 0.007); however, at the amino acid level CDS2 was the least variable (d = 0.001), whilst CDS5 remained the most variable (d = 0.013). This study describes the largest in-depth analysis of the C. trachomatis plasmid to date, through the analysis of plasmid sequence data mined from whole genome sequences spanning 50 years and from a worldwide distribution, providing insights into the nature and extent of existing variation within the plasmid as well as guidance for the design of future diagnostic assays. This is crucial at a time when single-target diagnostic assays are failing to detect natural mutants, putting those infected at risk of a serious long-term and life-changing illness
The Seasons / By James Thomson
No full textVorlageform des Erscheinungsvermerks: Leipzig Printed For John Sommer MDCCXCIV.Frontisp
User evaluation of a market-based recommender system
No full textRecommender systems have been developed for a wide variety of applications (ranging from books, to holidays, to web pages). These systems have used a number of different approaches, since no one technique is best for all users in all situations. Given this, we believe that to be effective, systems should incorporate a wide variety of such techniques and then some form of overarching framework should be put in place to coordinate them so that only the best recommendations (from whatever source) are presented to the user. To this end, in our previous work, we detailed a market-based approach in which various recommender agents competed with one another to present their recommendations to the user. We showed through theoretical analysis and empirical evaluation with simulated users that an appropriately designed marketplace should be able to provide effective coordination. Building on this, we now report on the development of this multi-agent system and its evaluation with real users. Specifically, we show that our system is capable of consistently giving high quality recommendations, that the best recommendations that could be put forward are actually put forward, and that the combination of recommenders performs better than any constituent recommende
Progress towards an inducible, replication-proficient transposon delivery vector for Chlamydia trachomatis
No full textBackgroundGenetic systems have been developed for Chlamydia but the extremely low transformationfrequency remains a significant bottleneck. Our goal is to develop aself-replicating transposon delivery vector for C. trachomatis which can be expanded prior to transposaseinduction.MethodsWe made E. coli/ C. trachomatis shuttle vectors bearing the Himar1 C9 transposase under control of the tet promoter and a novel rearrangement of the Himar1 transposon with the β-lactamase gene. Activity of the transposase was monitored by immunoblot and by DNA sequencing.ResultsWe constructed pSW2-mCh-C9, a C. trachomatis plasmid designed to act as aself-replicating vector carrying both the Himar1 C9 transposase under tet promoter control and its transposon. However, we were unable to recover this plasmid in C. trachomatis following multiple attempts attransformation.Therefore, we assembled two new deletion plasmidspSW2-mCh-C9-ΔTpon carrying only the Himar1 C9 transposase (under tet promoter control) and a sister vector (samesequence backbone) pSW2-mCh-C9-ΔTpase carrying its cognate transposon. Wedemonstrated that the biological components that make up both pSW2-mCh-C9-ΔTponand pSW2-mCh-C9-ΔTpase are active in E. coli. Both these plasmids could be independentlyrecovered in C. trachomatis.We attempted to perform lateral gene transfer bytransformation and mixed infection with C. trachomatis strains bearing pSW2-mCh-C9-ΔTpon and pSW2-RSGFP-Tpon (a green fluorescent version of pSW2-mCh-C9-ΔTpase). Despite success inachieving mixed infections, it was not possible to recover progeny bearing bothversions of these plasmids.ConclusionsWe have designed a self-replicating plasmid vectorpSW2-mCh-C9 for C. trachomatis carrying the Himar1 C9 transposase under tet promoter control. Whilst this can betransformed into E. coli it cannot be recovered in C. trachomatis. Based on selected deletions and phenotypicanalyses we conclude that low level expression from the tet inducible promoter is responsible forpremature transposition and hence plasmid loss early on in the transformationprocess.</p
Chrysis brevitarsis Thomson 1870
No full textChrysis brevitarsis THOMSON,1870 Chrysis brevitarsis THOMSON, 1870: 107. Holotype ♀; Sweden: Nerike [= Närke] (Lund). Chrysis brevitarsis: VAN DER SMISSEN 2010: 33 (key), 52 (descr., var. 1 and var. 2: Kazakhstan: Koniptau Mts., 100 km NW Taldi-Kurgan [= Taldykorgan]; 200 km NE Tcherkaskoe; var. 3: Kazakhstan: Issik 3 km S; Kyrgyzstan, env. Frunze [= Bishkek], 10 km Con Arik, 10 km W Taldi-Suu, 42,9° N 78,0° E (Issik-Kul); Tash-Arik, 11 km E Talas; Ala-Archa riv., Kashka- Suu, 1700m. Uzbekistan: Sukok). R e m a r k s: identification by VAN DER SMISSEN (2010) to be confirmed. The author listed three colour variations, without any mention to other characters. However, several similar blue species are distributed in Central Asia and another examination of those specimens is needed. D i s t r i b u t i o n: Kazakhstan, Kyrgyzstan, Uzbekistan.Published as part of Rosa, Paolo, 2019, A new remarkable species in the Chrysis ignita group (Hymenoptera, Chrysididae) and an overview on Central Asian species, with new synonymies, pp. 397-417 in Linzer biologische Beiträge 51 (1) on page 405, DOI: 10.5281/zenodo.375837
Complete Genome Sequence of the First KPC-Type Carbapenemase-Positive Proteus mirabilis Strain from a Bloodstream Infection
No full textSequencing of the blaKPC-positive strain Proteus mirabilis AOUC-001 was performed using both the MiSeq and PacBio RS II platforms and yielded a single molecule of 4,272,433 bp, representing the complete chromosome. Genome analysis showed the presence of several acquired resistance determinants, including two copies of blaKPC-2 carried on a fragment of a KPC-producing plasmid previously described in Klebsiella pneumoniae
Quantitative proteomics of the infectious and replicative forms of Chlamydia trachomatis
No full textThe obligate intracellular developmental cycle of Chlamydia trachomatis presents significant challenges in defining its proteome. In this study we have applied quantitative proteomics to both the intracellular reticulate body (RB) and the extracellular elementary body (EB) from C. trachomatis. We used C. trachomatis L2 as a model chlamydial isolate for our study since it has a high infectivity:particle ratio and there is an excellent quality genome sequence. EBs and RBs (>99% pure) were quantified by chromosomal and plasmid copy number using PCR, from which the concentrations of chlamydial proteins per bacterial cell/genome were determined. RBs harvested at 15h post infection (PI) were purified by three successive rounds of gradient centrifugation. This is the earliest possible time to obtain purified RBs, free from host cell components in quantity, within the constraints of the technology. EBs were purified at 48h PI. We then used two-dimensional reverse phase UPLC to fractionate RB or EB peptides before mass spectroscopic analysis, providing absolute amount estimates of chlamydial proteins. The ability to express the data as molecules per cell gave ranking in both abundance and energy requirements for synthesis, allowing meaningful identification of rate-limiting components. The study assigned 562 proteins with high confidence and provided absolute estimates of protein concentration for 489 proteins. Interestingly, the data showed an increase in TTS capacity at 15h PI. Most of the enzymes involved in peptidoglycan biosynthesis were detected along with high levels of muramidase (in EBs) suggesting breakdown of peptidoglycan occurs in the non-dividing form of the microorganism. All the genome-encoded enzymes for glycolysis, pentose phosphate pathway and tricarboxylic acid cycle were identified and quantified; these data supported the observation that the EB is metabolically active. The availability of detailed, accurate quantitative proteomic data will be invaluable for investigations into gene regulation and function
On a Mechanical Representation of Electric, Magnetic and Galvanic Forces, by William Thomson: a commented reading
No full textWe present and comment the homonimous article originally published by William Thomson, in 1847, in which the author explores the analogy between the estates of deformation in an elastic solid and the configurations of Faraday's lines of force. In this article Thomson has introduced for the first time the magnetic potential vector, associated in this context with rotational deformations in the solid. We present as well, the historical context in which Thomson's original paper has been conceived.Apresentamos e comentamos o artigo homônimo de William Thomson, originalmente publicado em 1847, no qual o autor explora a analogia entre os estados de deformação em um sólido elástico e as configurações das linhas de força de Faraday. Nele Thomson introduz pela primeira vez o potencial vetorial magnético, associando-o à deformação rotacional de um sólido. Apresentamos também um apanhado histórico do contexto dentro do qual o original de Thomson foi concebido
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