A quantitative account of genomic island acquisitions in prokaryotes

<p>Abstract</p> <p>Background</p> <p>Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness.</p> <p>In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species.</p> <p>Results</p> <p>When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor.</p> <p>Conclusions</p> <p>This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.</p

Assessment of the risk for rabies introduction and establishment in Lombok, Indonesia

Rabies, a zoonotic disease, is maintained in the domestic dog population in Indonesia and has caused human fatalities since its introduction to this country in the 1880s. Although rabies control strategies have been implemented on rabies-infected islands, this disease is still spreading to other parts of Indonesia, with newly infected islands as recent as 2012. Live dog movement on fishing or cargo boats is believed to have facilitated the introduction of rabies virus into previously rabies-free islands in Indonesia, such as to Bali and Flores. Until today, of the total 33 provinces, only nine provinces remain rabies-free including Lombok Island in West Nusa Tenggara (NTB) Province. This research was conducted from 2011 to 2013 to investigate pathways for rabies entry to Lombok Island via dog movement and to assess the probability of rabies entry and exposure to the susceptible dog population on Lombok. Further, this research aimed to provide knowledge of the pathways and probability of rabies entry to Lombok in order to inform development of quarantine and surveillance strategies to prevent rabies entry and establishment on Lombok. Pathways for rabies entry to Lombok were first defined based on the literature and then refined and prioritised based on expert opinion. After this process, two pathways of release of a rabiesinfected dog were identified: boat and ferry pathways. Scenario trees were developed for each pathway to describe the release of a rabies-infected dog to Lombok, as well as scenario trees to describe the exposure of a rabies-infected dog to the susceptible dog population on Lombok. Four surveys were conducted on Bali and Lombok islands to obtain data used to refine the pathways and to inform the release and exposure models. The first survey obtained data on dog numbers and dog management practices of dog owning households belonging to different ethnic groups at an urban site and a rural site on Lombok. A total of 400 households were interviewed, 300 at the urban site and 100 at the rural site. The majority of the interviewed households belonged to Balinese ethnic group. Sasakese households owning dogs were more frequent at the rural site compared to the urban site. Owning dogs born on Lombok was common (96% households), however, 4% of households reported owning dogs obtained from outside Lombok (Bali and Java). The latter was more common at the urban site and among Balinese ethnic group. All households that reported imported dogs mentionedtransporting the dog/s in a vehicle by ferry from Padang Bai harbour Bali to Lembar harbour Lombok. All these households also reported that the imported dogs did not have the documentation required by the quarantine agency and 11 reported that the imported dogs had been vaccinated but were not able to identify the type of vaccination. The dog owning households kept their dogs either fully restricted, semifree roaming or free-roaming but full restriction was reported only at the urban site. Dog bite cases were reported to be higher at the urban site. For the second survey, to investigate dog transportation on boats docking on Lombok, interviews were conducted with captains of boats that originated from other parts of Indonesia and of local Lombok boats at seven informal ports (no quarantine post). Over three consecutive days at each port, a total of 117 captains of outside boats and 52 captains of local boats were interviewed. This survey found that dogs are not common on boats. All of the captains interviewed, except one captain from Bali, reported never having a dog on board their boat. More than half (61.5%) of the captains of outside boats knew that rabies is transmitted to people through dog bites compared to only 7.7% of captains of local boats. Dog observation was also conducted during the survey visits to these ports to document the presence of dogs on boats, and the presence of dogs and interactions between people and dogs at the port area. No dogs were seen on boats, which confirmed the finding of the boat captain survey. To further investigate the role of illegal dog movement through ferry route, the thirdsurvey interviewed people travelling with a vehicle to Lombok by ferry from Padang Bai Bali. Interviews were conducted at Padang Bai harbour over ten days and 158 people were interviewed. The people interviewed consisted of Lombok residents (51.3%) and non-residents (48.7%); 10.8 % of which reported experience bringing dogs to Lombok. All of the 21 imported dogs were pedigree dogs; majority were male; and all had originated from Bali, Jakarta or West Java. Although these dogs were transported in several types of vehicles, the majority had been transported in a truck. Transportation for most of these dogs (14) was done at the request of dog owners living in Lombok and payment provided by the dog owners. Only two dogs werereported to have been vaccinated against rabies. None of the people who had transported these imported dogs reported the dogs undergoing quarantine inspection at either Padang Bai harbour or Lembar harbour Lombok. A fourth survey was undertaken to estimate the number of unowned dogs at the urban and rural sites on Lombok where the household survey was conducted. A photographic-recapture method was employed and the number of unowned dog was estimated using a Chapman estimate from Beck (1973). A higher number of unowned dogs was observed at the urban site than at the rural site. Information obtained from the surveys was incorporated into the risk assessment models to quantify the probability of that one rabies-infected dog is released at Lombok via boat and ferry pathway and the probability of a susceptible dog at the informal port, urban site and rural site becoming infected with rabies virus after the release of a rabies-infected dog via the boat and ferry pathway. Data from published literature and expert opinion were also utilised. Monte Carlo stochastic simulation modelling was performed with @Risk 6.0 (Palisade Corporation, USA). Each simulation consisted of 5,000 iterations sampled using the Latin hypercube method with a fixed random seed of one. Sensitivity analysis was also conducted to identify which input parameters were the most influential to the overall outputs of the release and exposure assessment models. This was performed using the @Risk 6.0 Advanced Sensitivity Analysis (Palisade Corporation, USA). Based on the results of this study, the probability of rabies being introduced into Lombok via both boat and ferry pathways was very low. However, these estimates were not negligible and to estimate the overall risk of virus introduction into Lombok for a specific period of time, the total number of boats, ferries and passengers in eachferry coming into Lombok should be considered. The sensitivity analyses for the release assessments indicate that the prevalence of rabies in Bali has a significant influence on the probability of rabies virus being introduced into Lombok. The presence of dogs on boats travelling to Lombok and the probability of ferry passengers bringing dogs to Lombok were also influential parameters. The exposure assessments suggest that the overall median probability of a rabid dog released in Lombok exposing and infecting a susceptible dog in Lombok was low. This probability was similar for a rabid dog being released at an informal Lombok port and for a rabid dog released by a person travelling in a ferry that resided in rural/urban Lombok. These results suggest that the probability of exposure is not negligible. The probability of the rabid dog confinement was an influential parameter on the probability of susceptible dogs in Lombok being exposed. These findings have provided information on pathways and probability forto Lombok and for rabies exposure to the susceptible dog population on Lombok. The practice of illegal dog movement via the ferry route can now be addressed to prevent rabies entry to Lombok, through rabies control at source (that is, on rabies-infected islands); improvement of performance of the quarantine agency ; and through education about rabies for the general public and dog owners as well as for animal health and public health officials. Preventing establishment in the event of rabies incursion through early disease detection and preparedness planning is also important. Early disease detection includes animal disease surveillance and monitoring the level of human dog bite cases. Preparedness can include responsible dog ownership that incorporates dog registration and identification, dog vaccination, neutering and confinement; dog population control through a better waste collection and disposal system by government agencies to reduce food sources for roaming dogs; and dog rabies vaccination for Lombok. In particular vaccination in advance of an incursion deserves serious consideration because it can create a barrier to prevent rabies transmission to people

REVISITING ANNA MOSCOWITZ\u27S KROSS\u27S CRITIQUE OF NEW YORK CITY\u27S WOMEN\u27S COURT: THE CONTINUED PROBLEM OF SOLVING THE PROBLEM OF PROSTITUTION WITH SPECIALIZED CRIMINAL COURTS

This article explores New York City\u27s non-traditional, judicially based response to prostitution. This article first recounts the history of New York City’s Women’s Court. It then examines the work of the Midtown Community Court, the “problem-solving court” established in 1993 to address criminal issues, like prostitution, in Midtown Manhattan. It also discusses the renewed concerns about sex work in New York and describe the movement, propelled by modern reformers, to address prostitution through specialty courts. It then contrasts the shared features and attributes of the Women’s Court and Midtown Court models. Finally, the article urges modern reformers to step back from the problem-solving court movement and their call for the creation of more such specialized criminal courts

To tax or to ban? A discrete choice experiment to elicit public preferences for phasing out glyphosate use in agriculture

In 2023, the European Union will vote on the reauthorization of glyphosate use, renewed in 2017 despite concern on impacts on the environment and public health. A ban is supported by several Member States but rejected by most farmers. What are citizens’ preferences to phase out glyphosate? To assess whether taxation could be an alternative to a ban, we conducted a discrete choice experiment in five European countries. Our results reveal that the general public is strongly willing to pay for a reduction in glyphosate use. However, while 75.5% of respondents stated to support a ban in the pre-experimental survey, experimental results reveal that in 73.35% of cases, earmarked taxation schemes are preferred when they lead to a strong reduction in glyphosate use for an increase in food price lower than that induced by a ban. When glyphosate reduction is balanced against its costs, a tax may be preferred

Detecting Horizontally Transferred and Essential Genes Based on Dinucleotide Relative Abundance

Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes

CRISPR Interference Directs Strand Specific Spacer Acquisition

Background: CRISPR/Cas is a widespread adaptive immune system in prokaryotes. This system integrates short stretches of DNA derived from invading nucleic acids into genomic CRISPR loci, which function as memory of previously encountered invaders. In Escherichia coli, transcripts of these loci are cleaved into small RNAs and utilized by the Cascade complex to bind invader DNA, which is then likely degraded by Cas3 during CRISPR interference. Results: We describe how a CRISPR-activated E. coli K12 is cured from a high copy number plasmid under non-selective conditions in a CRISPR-mediated way. Cured clones integrated at least one up to five anti-plasmid spacers in genomic CRISPR loci. New spacers are integrated directly downstream of the leader sequence. The spacers are non-randomly selected to target protospacers with an AAG protospacer adjacent motif, which is located directly upstream of the protospacer. A cooccurrence of PAM deviations and CRISPR repeat mutations was observed, indicating that one nucleotide from the PAM is incorporated as the last nucleotide of the repeat during integration of a new spacer. When multiple spacers were integrated in a single clone, all spacer targeted the same strand of the plasmid, implying that CRISPR interference caused by the first integrated spacer directs subsequent spacer acquisition events in a strand specific manner. Conclusions: The E. coli Type I-E CRISPR/Cas system provides resistance against bacteriophage infection, but also enables removal of residing plasmids. We established that there is a positive feedback loop between active spacers in a cluster – i

N-gram analysis of 970 microbial organisms reveals presence of biological language models

<p>Abstract</p> <p>Background</p> <p>It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word usage indicative of authors or topics, and that the algorithms originally developed for natural language processing may therefore be applied to genome sequences to draw biologically relevant conclusions. Following this approach of 'biological language modeling', statistical n-gram analysis has been applied for comparative analysis of whole proteome sequences of 44 organisms. It has been shown that a few particular amino acid n-grams are found in abundance in one organism but occurring very rarely in other organisms, thereby serving as genome signatures. At that time proteomes of only 44 organisms were available, thereby limiting the generalization of this hypothesis. Today nearly 1,000 genome sequences and corresponding translated sequences are available, making it feasible to test the existence of biological language models over the evolutionary tree.</p> <p>Results</p> <p>We studied whole proteome sequences of 970 microbial organisms using n-gram frequencies and cross-perplexity employing the Biological Language Modeling Toolkit and Patternix Revelio toolkit. Genus-specific signatures were observed even in a simple unigram distribution. By taking statistical n-gram model of one organism as reference and computing cross-perplexity of all other microbial proteomes with it, cross-perplexity was found to be predictive of branch distance of the phylogenetic tree. For example, a 4-gram model from proteome of <it>Shigellae flexneri 2a</it>, which belongs to the <it>Gammaproteobacteria </it>class showed a self-perplexity of 15.34 while the cross-perplexity of other organisms was in the range of 15.59 to 29.5 and was proportional to their branching distance in the evolutionary tree from <it>S. flexneri</it>. The organisms of this genus, which happen to be pathotypes of <it>E.coli</it>, also have the closest perplexity values with <it>E. coli.</it></p> <p>Conclusion</p> <p>Whole proteome sequences of microbial organisms have been shown to contain particular n-gram sequences in abundance in one organism but occurring very rarely in other organisms, thereby serving as proteome signatures. Further it has also been shown that perplexity, a statistical measure of similarity of n-gram composition, can be used to predict evolutionary distance within a genus in the phylogenetic tree.</p