Direct detection of methylation in genomic DNA

The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N(6)-methyladenine, 5-methylcytosine and N(4)-methylcytosine. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. It was previously shown that N(6)-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. We extended this method to include N(4)-methylcytosine detection in both in vitro and in vivo methylated DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. This provides the possibility to define the complete methylome of any prokaryote

ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes

This is the final version of the article. Available from the publisher via the DOI in this record.Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl.MWJvP is funded by the Netherlands Organization for Scientific Research (NWO) via a VENI grant. TtB and MAvD are funded by the BioAssist/BRS programme of the Netherlands Bioinformatics Centre, which is supported by the Netherlands Genomics Initiative. This work is part of the programme of BiG Grid, the Dutch e-Science Grid, which is financially supported by the NWO. MV is supported by investment from the European Regional Development Fund and the European Social Fund Convergence Programme for Cornwall and the Isles of Scilly to the European Centre for the Environment and Human Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Eat or be eaten? An observation of Podarcis erhardii consuming Scolopendra cingulata from Andros Island, Cyclades, Greece

Podarcis wall lizards mainly feed on coleopterans, orthopterans, arachnids, and other small invertebrates. However, Aegean wall lizards, Podarcis erhardii, are widely distributed across Aegean islands and are increasingly observed eating non-traditional food items ranging from plant material to conspecific eggs and body parts. Here, we report the first documented case of P. erhardii consuming a large centipede, Scolopendra cingulata. The predator-prey relationship between these species has appeared to go both ways and may intensify on islands

Promoter propagation in prokaryotes

Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. In many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large impact on rapid adaptation of novel or cryptic functions. Querying all publicly available prokaryotic genomes (1362) uncovered >4000 families of highly conserved PMPs (50 to 100 long with =80% nt identity) in 1043 genomes from 424 different genera. The genomes with the largest number of PMP families are Anabaena variabilis (28 families), Geobacter uraniireducens (27 families) and Cyanothece PCC7424 (25 families). Family size varied from 2 to 93 homologous promoters (in Desulfurivibrio alkaliphilus). Some PMPs are present in particular species, but some are conserved across distant genera. The identified PMPs represent a conservative dataset of very recent or conserved events of mobilization of non-coding DNA and thus they constitute evidence of an extensive reservoir of recyclable regulatory sequences for rapid transcriptional rewirin

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

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons

Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons. M. leprae’s genome includes 1133 pseudogenes and 1614 protein-coding genes and can be compared with the close genome of M. tuberculosis. Assuming M. leprae’s pseudogenes to represent dispensable genes, we have studied the position of these pseudogenes in the operons of M. leprae and of their orthologs in M. tuberculosis. We observed that both tend to be located in the 3′ (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). Analysis of pseudogenes in all available prokaryotic genomes confirms this trend (P-value of 7.1 × 10−7). In a complementary analysis, we found a significant tendency for essential genes to be located at the 5′ (upstream) half of the operon (P-value of 0.006). Our work provides an indication that, in prokarya, functionally less important genes have a tendency to be located at the end of operons, while more relevant genes tend to be located toward operon starts

The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes

Peer reviewe

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

Bronnen van antibioticaresistentie in het milieu en mogelijke maatregelen

Het RIVM heeft in samenwerking met andere instituten onderzocht hoeveel resistente bacteriën via afvalwater in het Nederlandse oppervlaktewater terechtkomen. Afvalwater is, naast mest, de belangrijkste bron waardoor antibioticaresistente bacteriën in het milieu belanden. In 60 tot 100% van het onderzochte afvalwater zitten bijzonder resistente micro-organismen(BMRO), zoals ESBL-producerende E. coli en carbapenemresistente Enterobacteriaceae. Daarnaast zijn resten van antibiotica in het afvalwater gevonden. Mensen kunnen aan resistente bacteriën in het milieu worden blootgesteld, bijvoorbeeld als zij in contact komen met water waarop gezuiverd afvalwater wordt geloosd. Vooralsnog is het onduidelijk hoe groot de bijdrage van deze blootstelling is ten opzichte van andere blootstellingsroutes, en wat de gevolgen daarvan voor de volksgezondheid zijn. Daarvoor wordt aanvullend onderzoek aanbevolen. Duidelijk is wel dat mensen naast blootstelling via het milieu, ook door andere bronnen kunnen worden blootgesteld aan antibioticaresistente bacteriën, bijvoorbeeld tijdens reizen naar landen in Azië of Zuid-Amerika. Door de huidige behandeling van afvalwater nemen de concentraties van antibioticaresistente bacteriën af. Er bestaan aanvullende zuiveringstechnieken voor afvalwater die het aantal antibioticaresistente bacteriën in het oppervlaktewater nog verder kunnen verminderen. Ook de concentraties van resistente bacteriën in mest kunnen door aanvullende zuiveringstechnieken verminderd worden.In collaboration with other institu tions , RIVM investigated how many resistant bacteria enter Dutch surface water s from waste water treatment plants. Next to manure, waste water is the main source of resistant bacteria in the environment. Resistant bacteria of particular public health concern, including ESBL -producing E. coli and carbapenem resistant Enterobacteriace ae, have been found in 60 -100% of all investigated waste water samples. Antibiotics themselves have also been found in waste water. Human exposure to resistant bacteria is possible, for example, upon contact with surface water which receives waste water treatment plant effluent. So far, the contribution of this exposure to the total exposure to resistant bacteria is unknown, as are the effects of this exposure on public health. Additional research is therefore recommended. Humans can also be exposed to resistant bacteria via other routes, such as travel to Asian or Latin American. The current treatment of waste water reduces the concen trations of resistant bacteria. Advanced techniques are available which can decrease the amounts of resistant bacteria further. Options for the reduction of resistant bacteria also exist for the treatment of manure