Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database

According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDITOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water

An alien ectosymbiotic branchiobdellidan (Annelida: Clitellata) adopting exotic crayfish: a biological co-invasion with unpredictable consequences

Invasive alien species present a global threat to biodiversity, particularly where pathogens and symbionts are involved. Branchiobdellidans are clitellate annelids with an obligate ectosymbiotic association primarily on astacoidean crayfish. There are several examples of branchiobdellidan species adopting a geographically exotic host where endemic and exotic crayfishes cohabit the same water body. The first records of a western North American branchiobdellidan, Xironogiton victoriensis, adopting the eastern North American crayfish, Procambarus clarkii, in 2 river basins in Spain provide further evidence of the ectosymbionts’ tolerance to adopt an exotic host. Given worldwide translocations of these and other commercial crayfish species, limnologists and agency managers need to be alert for further introductions of X. victoriensis and other branchiobdellidans. Impacts of these exotic ectosymbionts on habitat and biota at a new location are unknown, as are their consequences on native biodiversit

A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)

In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysisThis work has also been supported by grants BFU2012-39816-C02-01 (co-financed by FEDER funds and the Ministry of Economy and Competitiveness, Spain) to AL and Prometeo/2009/092 (Ministry of Education, Government of Valencia, Spain) and Explora Ciencia y Explora Tecnologia/SAF2013-49788-EXP (Spanish Ministry of Economy and Competitiveness) to AM. IRF is recipient of a "Sara Borrell" postdoctoral fellowship (Ref. CD12/00492) from the Ministry of Economy and Competitiveness (Spain). We are also grateful to the Spanish Network for the Study of Plasmids and Extrachromosomal Elements (REDEEX) for encouraging and funding cooperation among Spanish microbiologists working on the biology of mobile genetic elements (Spanish Ministry of Science and Innovation, reference number BFU2011-14145-E).Campos Frances, M.; Llorens, C.; Sempere Luna, JM.; Futami, R.; Rodríguez, I.; Carrasco, P.; Capilla, R.... (2015). A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biology Direct. 10(41):1-13. https://doi.org/10.1186/s13062-015-0070-9S1131041Baquero F, Coque TM, Canton R. Counteracting antibiotic resistance: breaking barriers among antibacterial strategies. Expert Opin Ther Targets. 2014;18:851–61.Baquero F, Lanza VF, Canton R, Coque TM. Public health evolutionary biology of antimicrobial resistance: priorities for intervention. Evol Appl. 2014;8:223–39.Baquero F, Coque TM, de la Cruz F. 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Clin Microbiol Infect. 2012;18 Suppl 4:2–4.Kumsa B, Socolovschi C, Parola P, Rolain JM, Raoult D. Molecular detection of Acinetobacter species in lice and keds of domestic animals in Oromia Regional State. Ethiopia PLoS One. 2012;7:e52377.Ahmad A, Ghosh A, Schal C, Zurek L. Insects in confined swine operations carry a large antibiotic resistant and potentially virulent enterococcal community. BMC Microbiol. 2011;11:23.Graczyk TK, Knight R, Gilman RH, Cranfield MR. The role of non-biting flies in the epidemiology of human infectious diseases. Microbes Infect. 2001;3:231–5.Limoee M, Enayati AA, Khassi K, Salimi M, Ladonni H. Insecticide resistance and synergism of three field-collected strains of the German cockroach Blattella germanica (L.) (Dictyoptera: Blattellidae) from hospitals in Kermanshah, Iran. Trop Biomed. 2011;28:111–8.Salehzadeha A, Tavacolb P, Mahjubc H. Bacterial, fungal and parasitic contamination of cockroaches in public hospitals of Hamadan, Iran. J Vect Borne Dis. 2007;44:105–10.Akinjogunla OJ, Odeyemi AT, Udoinyang EP. Cockroaches (periplaneta americana and blattella germanica): reservoirs of multi drug resistant (MDR) bacteria in Uyo, Akwa Ibom State. Scientific J Biol Sci. 2012;1:19–30.Mideo N, Alizon S, Day T. Linking within- and between-host dynamics in the evolutionary epidemiology of infectious diseases. Trends Ecol Evol. 2008;23:511–7.Gillings MR, Stokes HW. Are humans increasing bacterial evolvability? Trends EcolEvol. 2012;27:346–52.Baquero F. Environmental stress and evolvability in microbial systems. Clin Microbiol Infect. 2009;15 Suppl 1:5–10.Paun G, Rozemberg G, Salomaa A. The Oxford Handbook of Membrane Computing. Oxford, London. Oxford University Press. 2010.Paun G. Membrane Computing. An Introduction. Berlin, Heidelberg. Springer-Verlag GmbH. 2002.Paun G. Computing with membranes. J Comput Syst Sci. 2000;61:108–43.Fontana F, Biancom L, Manca V. P systems and the modeling of biochemical oscillations. 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Alpine bogs of southern Spain show human-induced environmental change superimposed on long-term natural variations

Recent studies have proved that high elevation environments, especially remote wetlands, are exceptional ecological sensors of global change. For example, European glaciers have retreated during the 20th century while the Sierra Nevada National Park in southern Spain witnessed the first complete disappearance of modern glaciers in Europe. Given that the effects of climatic fluctuations on local ecosystems are complex in these sensitive alpine areas, it is crucial to identify their long-term natural trends, ecological thresholds, and responses to human impact. In this study, the geochemical records from two adjacent alpine bogs in the protected Sierra Nevada National Park reveal different sensitivities and long-term environmental responses, despite similar natural forcings, such as solar radiation and the North Atlantic Oscillation, during the late Holocene. After the Industrial Revolution both bogs registered an independent, abrupt and enhanced response to the anthropogenic forcing, at the same time that the last glaciers disappeared. The different response recorded at each site suggests that the National Park and land managers of similar regions need to consider landscape and environmental evolution in addition to changing climate to fully understand implications of climate and human influence.This study was supported by the project P11-RNM 7332 of the “Junta de Andalucía”, the projects CGL2013-47038-R and CGL2015-67130-C2-1-R of the “Ministerio de Economía y Competitividad of Spain and Fondo Europeo de Desarrollo Regional FEDER” and the research group RNM0190 and RNM309 (Junta de Andalucía). A.G.-A. was also supported by a Marie Curie Intra-European Fellowship of the 7th Framework Programme for Research, Technological Development and Demonstration of the European Commission (NAOSIPUK. Grant Number: PIEF-GA-2012-623027) and by a Ramón y Cajal Fellowship RYC-2015-18966 of the Spanish Government (Ministerio de Economía y Competividad). J.L.T. was also supported by a Small Research Grant by the Carnegie Trust for the Universities of Scotland and hosted the NAOSIPUK project (PIEF-GA-2012-623027). M. J. R-R acknowledges the PhD funding provided by Consejería de Economía, Innovación, Ciencia y Empleo de la Junta de Andalucía (P11-RNM 7332)

Rise and demise of the global silver standard

In the early modern period, the world economy gravitated around the expansion of long-distance commerce. Together with navigation improvements, silver was the prime commodity which moved the sails of such trade. The disparate availability and the particular demand for silver across the globe determined the participation of producers, consumers, and intermediaries in a growing global economy. American endowments of silver are a known feature of this process; however, the fact that the supply of silver was in the form of specie is a less known aspect of the integration of the global economy. This chapter surveys the production and export of silver specie out of Spanish America, its intermediation by Europeans, and the reexport to Asia. It describes how the sheer volume produced and the quality and consistency of the coin provided familiarity with, and reliability to, the Spanish American peso which made it current in most world markets. By the eighteenth century, it has become a currency standard for the international economy which grew together with the production and coinage of silver. Implications varied according to the institutional settings to deal with specie and foreign exchange in each intervening economy of that trade. Generalized warfare in late eighteenth-century Europe brought down governance in Spanish America and coinage fragmented along with the political fragmentation of the empire. The emergence of new sovereign republics and the end of minting as known meant the cessation of the silver standard that had contributed to the early modern globalization

Performance and Operation of the CMS Electromagnetic Calorimeter

The operation and general performance of the CMS electromagnetic calorimeter using cosmic-ray muons are described. These muons were recorded after the closure of the CMS detector in late 2008. The calorimeter is made of lead tungstate crystals and the overall status of the 75848 channels corresponding to the barrel and endcap detectors is reported. The stability of crucial operational parameters, such as high voltage, temperature and electronic noise, is summarised and the performance of the light monitoring system is presented

Genotyping of black grouse MHC class II B using reference Strand-Mediated Conformational Analysis (RSCA)

<p>Abstract</p> <p>Background</p> <p>The Major Histocompatibility Complex (MHC) is a cluster of genes involved in the vertebrate immune system and includes loci with an extraordinary number of alleles. Due to the complex evolution of MHC genes, alleles from different loci within the same MHC class can be very similar and therefore difficult to assign to separate loci. Consequently, single locus amplification of MHC genes is hard to carry out in species with recently duplicated genes in the same MHC class, and multiple MHC loci have to be genotyped simultaneously. Since amplified alleles have the same length, accurate genotyping is difficult. Reference Strand-Mediated Conformational Analysis (RSCA), which is increasingly used in studies of natural populations with multiple MHC genes, is a genotyping method capable to provide high resolution and accuracy in such cases.</p> <p>Findings</p> <p>We adapted the RSCA method to genotype multiple MHC class II B (BLB) genes in black grouse (<it>Tetrao tetrix</it>), a non-model galliform bird species, using a 96-Capillary Array Electrophoresis, the MegaBACE™ 1000 DNA Analysing System (GE Healthcare). In this study we used fluorescently labelled reference strands from both black grouse and hazel grouse and observed good agreement between RSCA and cloning/sequencing since 71 alleles were observed by cloning/sequencing and 76 alleles by RSCA among the 24 individuals included in the comparison. At the individual level however, there was a trend towards more alleles scored with RSCA (1-6 per individual) than cloning/sequencing (1-4 per individual). In 63% of the pair-wise comparison, the identical allele was scored in RSCA as in cloning/sequencing. Nine out of 24 individuals had the same number of alleles in RSCA as in cloning/sequencing. Our RSCA protocol allows a faster RSCA genotyping than presented in many other RSCA studies.</p> <p>Conclusions</p> <p>In this study, we have developed the RSCA typing method further to work on a 96-Capillary Array Electrophoresis (MegaBACE™ 1000). Our RSCA protocol can be applied to fast and reliable screening of MHC class II B diversity of black grouse populations. This will facilitate future large-scale population studies of black grouse and other galliformes species with multiple inseparable MHC loci.</p