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Background Alignment-free methods are a popular approach for comparing biological sequences, including complete genomes. The methods range from probability distributions of sequence composition to first and higher-order Markov chains, where a k -th order Markov chain over DNA has 4 k formal parameters. To circumvent this exponential growth in parameters, variable-length Markov chains (VLMCs) have gained popularity for applications in molecular biology and other areas. VLMCs adapt the depth depending on sequence context and thus curtail excesses in the number of parameters. The scarcity of available fast, or even parallel software tools, prompted the development of a parallel implementation using lazy suffix trees and a hash-based alternative. Results An extensive evaluation was performed on genomes ranging from 12Mbp to 22Gbp. Relevant learning parameters were chosen guided by the Bayesian Information Criterion (BIC) to avoid over-fitting. Our implementation greatly improves upon the state-of-the-art even in serial execution. It exhibits very good parallel scaling with speed-ups for long sequences close to the optimum indicated by Amdahl’s law of 3 for 4 threads and about 6 for 16 threads, respectively. Conclusions Our parallel implementation released as open-source under the GPLv3 license provides a practically useful alternative to the state-of-the-art which allows the construction of VLMCs even for very large genomes significantly faster than previously possible. Additionally, our parameter selection based on BIC gives guidance to end-users comparing genomes.

Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species. Plasmids are present in many bacteria and are often transferred between different species causing horizontal gene transfer. By comparing the sequences of 25 plasmid DNA backbones, the authors show that homologous recombination is prevalent in plasmids and that the plasmids have adapted to persist in different host bacteria.

The finance industry is required to respond to public criticism of perceived immoral behaviour. To create legitimacy, financial firms not only undertake corporate social responsibility (CSR) activities, but also support such activities with precise justifications. In this paper, we study CSR justifications appearing in annual and sustainability reports from the Swedish finance industry. Our objective is to investigate the ethical character of CSR justifications in the finance industry. This is an interesting topic, both because CSR carries ethical meaning and because CSR justifications play a role in actual business activities. A secondary aim of this article is to test whether decoupled corporate claims about CSR can be recoupled, which would potentially help companies to act responsibly. The observed CSR justifications avoided the fundamental question of whether the finance industry does in fact have responsibilities, and they did not manifest awareness of stakeholders' demands for CSR. Seemingly value-based CSR activities often lacked ethical justifications. These characteristics do not harmonize with the responsible image that the contemporary finance industry wants to portray. Our counterintuitive finding is that amorality prevails in the justifications that banks give for undertaking CSR activities.

The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.

In preparing Melville’s copy of William Rounseville Alger’s The Solitudes of Nature and of Man (Boston: Roberts, 1867) for mounting at Melville’s Marginalia Online , the transcription of one of Melville’s annotations was corrected to reveal a direct reference to Claude Fleury’s The Ecclesiastical History of M. L’ Abbé Fleury (Oxford: Rivingston, London, 1842). Fleury’s Ecclesiastical History adds to the evidence of Melville’s comprehensive study of religious history in the Near East while composing Clarel , a course of study comparable to that which his eponymous protagonist would have received in divinity school. Melville’s annotation identifies Fleury’s history as the source for Alger’s reference to Arsenius the Great, an ascetic monk who fled the court of the Emperor Arcadius, joined a desert monastery and “for fifty years made his life one long solitary prayer” ( MMO Alger 180). Melville’s familiarity with Fleury’s history adds to the evidence of his interest in hagiography and the relationship between ascetic practices and aesthetic theory. As he continued to study poetry and aesthetics in the latter stages of his career, ascetic practices and aesthetic contemplation were increasingly interrelated in Melville’s conception of the creation and experience of art.

The genomic signature of an organism captures the characteristics of repeated oligonucleotide patterns in its genome 1 , such as oligomer frequencies, GC content, and differences in codon usage. Viruses, however, are obligate intracellular parasites that are dependent on their host cells for replication, and information about genomic signatures in viruses has hitherto been sparse. Here, we investigate the presence and specificity of genomic signatures in 2,768 eukaryotic viral species from 105 viral families, aiming to illuminate dependencies and selective pressures in viral genome evolution. We demonstrate that most viruses have highly specific genomic signatures that often also differ significantly between species within the same family. The species-specificity is most prominent among dsDNA viruses and viruses with large genomes. We also reveal consistent dissimilarities between viral genomic signatures and those of their host cells, although some viruses present slight similarities, which may be explained by genetic adaptation to their native hosts. Our results suggest that significant evolutionary selection pressures act upon viral genomes to shape and preserve their genomic signatures, which may have implications for the field of synthetic biology in the construction of live attenuated vaccines and viral vectors. Genomic analysis of 2,768 viral species reveals conserved and distinct genome-wide differences in specific oligonucleotide patterns, so-called genomic signatures. These are likely caused by various selection pressures acting on viral genomes.

The complete nucleotide sequence of plasmids pMCBF1 and pMCBF6 was determined and analyzed. pMCBF1 and pMCBF6 form a novel clade within the IncP-1 plasmid family designated IncP-1 ς. The plasmids were exogenously isolated earlier from a marine biofilm. pMCBF1 (62 689 base pairs; bp) and pMCBF6 (66 729 bp) have identical backbones, but differ in their mercury resistance transposons. pMCBF1 carries Tn5053 and pMCBF6 carries Tn5058. Both are flanked by 5 bp direct repeats, typical of replicative transposition. Both insertions are in the vicinity of a resolvase gene in the backbone, supporting the idea that both transposons are \"res-site hunters\" that preferably insert close to and use external resolvase functions. The similarity of the backbones indicates recent insertion of the two transposons and the ongoing dynamics of plasmid evolution in marine biofilms. Both plasmids also carry the insertion sequence ISPst1, albeit without flanking repeats. ISPs1is located in an unusual site within the control region of the plasmid. In contrast to most known IncP-1 plasmids the pMCBF1/pMCBF6 backbone has no insert between the replication initiation gene (trfA) and the vegetative replication origin (oriV). One pMCBF1/pMCBF6 block of about 2.5 kilo bases (kb) has no similarity with known sequences in the databases. Furthermore, insertion of three genes with similarity to the multidrug efflux pump operon mexEF and a gene from the NodT family of the tripartite multi-drug resistance-nodulation-division (RND) system in Pseudomonas aeruginosa was found. They do not seem to confer antibiotic resistance to the hosts of pMCBF1/pMCBF6, but the presence of RND on promiscuous plasmids may have serious implications for the spread of antibiotic multi-resistance.

Herpes simplex virus type 1 (HSV-1) and varicella zoster virus (VZV) are closely related viruses causing lifelong infections. They are typically associated with mucocutaneous or skin lesions, but may also cause severe neurological or ophthalmic diseases, possibly due to viral- and/or host-genetic factors. Although these viruses are well characterized, genome-wide evolutionary studies have hitherto only been presented for VZV. Here, we present a genome-wide study on HSV-1. We also compared the evolutionary characteristics of HSV-1 with those for VZV. We demonstrate that, in contrast to VZV for which only a few ancient recombination events have been suggested, all HSV-1 genomes contain mosaic patterns of segments with different evolutionary origins. Thus, recombination seems to occur extremely frequent for HSV-1. We conclude by proposing a timescale for HSV-1 evolution, and by discussing putative underlying mechanisms for why these otherwise biologically similar viruses have such striking evolutionary differences.

Replication of herpes simplex virus 1 is coupled to recombination, but the molecular mechanisms underlying this process are poorly characterized. The role of Rad51 and Rad52 recombinases in viral recombination was examined in human fibroblast cells 1BR.3.N (wild type) and in GM16097 with replication defects caused by mutations in DNA ligase I. Intermolecular recombination between viruses, tsS and tsK, harboring genetic markers gave rise to ∼17% recombinants in both cell lines. Knock-down of Rad51 and Rad52 by siRNA reduced production of recombinants to 11% and 5%, respectively, in wild type cells and to 3% and 5%, respectively, in GM16097 cells. The results indicate a specific role for Rad51 and Rad52 in recombination of replicating herpes simplex virus 1 DNA. Mixed infections using clinical isolates with restriction enzyme polymorphisms in the US4 and US7 genes revealed recombination frequencies of 0.7%/kbp in wild type cells and 4%/kbp in GM16097 cells. Finally, tandem repeats in the US7 gene remained stable upon serial passage, indicating a high fidelity of recombination in infected cells.

Three synthesis routes are presented here that leads to carbon–silica composites. These were characterized by nitrogen physisorption, by thermogravimetric analysis and by dynamic toluene adsorption test similar to Ashrae standard I45.1. The carbon–silica composites possess high microporosity and mesoporosity as well as large surface areas. Furthermore, the control of the microporosity as well as pore size distribution is possible because they depend on the amount of carbon used and of the synthesis route. Following routes I and III a wide micro-mesoporous pore size (1–32 nm) was obtained where as by route II narrow micro-mesoporous pore size (1–4 nm) was observed. In addition, pore diameters center in the range of 1.13–1.17 nm was observed when carbon content was 32 or 45 wt%. The dynamic adsorption of toluene was evaluated for carbon–silica composites obtained by three preparation routes at two different carbon contents, 32 and 45 wt% The results showed that a composite with 45 wt% carbon content and obtained via preparation route I gave the highest toluene adsorption capacity (27.6 wt% relative to carbon content). The large uptake capacity of this composite was attributed to the presence of high microporosity volume and a wide (1–32 nm) bimodal pore system consisting of extensive mesopore channels (2–32 nm) as well as large surface area. These capacity values of carbon–silica composites are by weight relative to carbon content and are competitive to, results obtained for commercial coconut activated carbon (31.1 wt%) and significantly better than a commercial alumina-carbon composite (9.5 wt%) at 0% efficiency.