The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.     

Comparative study of four sigmoid models of pressure-volume curve in acute lung injury

Background  

The pressure-volume curve of the respiratory system is a tool to monitor and set mechanical ventilation in acute lung injury. Mathematical models of the static pressure-volume curve of the respiratory system have been proposed to overcome the inter- and intra-observer variability derived from eye-fitting. However, different models have not been compared.     

Genomic Regions Conserved in Lineage II Escherichia coli O157:H7 Strains

Populations of the food- and waterborne pathogen Escherichia coli O157:H7 are comprised of two major lineages. Recent studies have shown that specific genotypes within these lineages differ substantially in the frequencies with which they are associated with human clinical disease. While the nucleotide sequences of the genomes of lineage I strains E. coli O157 Sakai and EDL9333 have been determined, much less is known about the genomes of lineage II strains. In this study, suppression subtractive hybridization (SSH) was used to identify genomic features that define lineage II populations. Three SSH experiments were performed, yielding 1,085 genomic fragments consisting of 811 contigs. Bacteriophage sequences were identified in 11.3% of the contigs, 9% showed insertions and 2.3% deletions with respect to E. coli O157:H7 Sakai, and 23.2% did not have significant identity to annotated sequences in GenBank. In order to test for the presence of these novel loci in lineage I and II strains, 27 PCR primer sets were designed based on sequences from these contigs. All but two of these PCR targets were found in the majority (51.9% to 100%) of 27 lineage II strains but in no more than one (<6%) of the 17 lineage I strains. Several of these linage II-related fragments contain insertions/deletions that may play an important role in virulence. These lineage II-related loci were also shown to be useful markers for genotyping of E. coli O157:H7 strains isolated from human and animal sources.Enterohemorrhagic Escherichia coli is associated with diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome in humans (31). E. coli serotype O157:H7 predominates in epidemics and sporadic cases of enterohemorrhagic E. coli-related infections in the United States, Canada, Japan, and the United Kingdom (12). Cattle are considered the most important reservoir of E. coli O157:H7 (10, 24, 37, 41), and foods contaminated with bovine feces are thought to be the most common source of human infection with this pathogen (27, 33). The two most important virulence factors of the organism are the production of one or more Shiga toxins (Stx) (6, 20, 32) and the ability to attach to and efface microvilli of host intestinal cells (AE). Stx genes are encoded by temperate bacteriophage inserted in the bacterial chromosome, and genes responsible for the AE phenotype are located on the locus of enterocyte effacement (LEE) as well as other pathogenicity islands (4, 17). All E. coli O157:H7 strains also possess a large plasmid which is thought to play a role in virulence (10, 40, 42).Octamer-based genome scanning (OBGS) was first used to show that E. coli O157 strains from the United States and Australia could be subdivided into two genetically distinct lineages (21, 22, 46). While both E. coli O157:H7 lineages are associated with human disease and are isolated from cattle, there is a bias in the host distribution between the two lineages, with a significantly higher proportion of lineage I strains isolated from humans than lineage II strains. Several recent studies have shown that there are inherent differences in gene content and expression between populations of lineage I and lineage II E. coli O157:H7 strains. Lejeune et al. (26) reported that the antiterminator Q gene of the stx₂-converting bacteriophage 933W was found in all nine OBGS lineage I strains examined but in only two of seven lineage II strains, suggesting that there may be lineage-specific differences in toxin production. Dowd and Ishizaki (9) used DNA microarray analysis to examine expression of 610 E. coli O157:H7 genes and showed that lineage I and lineage II E. coli O157:H7 strains have evolved distinct patterns of gene expression which may alter their virulence and their ability to survive in different microenvironments and colonize the intestines of different hosts (9, 28, 38).The observations of lineage host bias have been supported and extended by studies using a six-locus-based multiplex PCR termed the lineage-specific polymorphism assay (LSPA-6) (46). However, Ziebell et al. (48) have recently shown that not all LSPA-6 types within lineage II are host biased; e.g., LSPA-6 type 211111 isolation rates from humans and cattle were significantly different from those of other lineage II LSPA-6 types. Therefore, a clearer definition is required of not only the differences between lineages but also the differences among clonal groups within lineages.The genome sequences of two E. coli O157:H7 strains, Sakai and EDL933 (14, 36), have been determined; however, both of these strains are of lineage I, and there are presently no completed and fully annotated genome sequences available for lineage II strains. In our laboratory, comparative studies utilizing suppression subtractive hybridization (SSH) and comparative genomic hybridization revealed numerous potential virulence factors that are conserved in lineage I strains and that are rare or absent in lineage II strains (42, 47). In this study, we have used SSH to identify genomic regions present in E. coli O157:H7 lineage II strains that are absent from lineage I strains. We wished to examine the distribution of these novel gene segments in E. coli O157:H7 strains and gain insight into their origins and functions. We also attempted to identify molecular markers specific to lineage II strains as well as other markers that would be useful in the genetic subtyping or molecular fingerprinting of E. coli O157:H7 strains in population and epidemiological studies (25). This information may be helpful in the identification of genotypes of the organism associated with specific phenotypes of both lesser and greater virulence (29).     

Cardiorespiratory and minimum alveolar concentration sparing effects of a continuous intravenous infusion of dexmedetomidine in halothane or isoflurane-anaesthetized rats

Dexmedetomidine (DEX) is a highly selective alpha(2)-adrenoceptor agonist in both the central and peripheral nervous systems. Its cardiorespiratory effects have been described; however, these effects have not been reported when it is used in combination with volatile anaesthetics in rats. The cardiovascular and respiratory actions of a continuous intravenous infusion of 0.25 microg/kg/min of DEX administered to rats anaesthetized at 1 minimum alveolar concentration (MAC) of either halothane (HAL) or isoflurane (ISO) were studied. Twenty-eight rats were grouped into four treatment groups: HAL alone, ISO alone, DEX + HAL and DEX + ISO. The MAC(HAL) or MAC(ISO) was determined in each rat from alveolar gas samples at the time of tail clamping. Control MAC values, expressed as mean +/- standard deviation, were 1.31 +/- 0.1% for HAL and 1.46 +/- 0.05% for ISO. DEX reduced HAL MAC from 1.31 +/- 0.1% to 0.36 +/- 0.22% (72 +/- 17% MAC reduction) and ISO MAC from 1.46 +/- 0.05% to 0.83 +/- 0.2% (43 +/- 14% MAC reduction). Heart rate (HR) was decreased in both DEX groups at 1 MAC, with no differences between HAL and ISO. The mean arterial pressure was significantly depressed in the DEX + ISO group compared with the ISO only group. This difference in mean arterial blood pressure (MABP) was not seen between the DEX + HAL and HAL only groups. Respiratory depression was minor at 1 MAC with both inhalant anaesthetics. DEX reduced the MAC of HAL to a degree greater than it decreased the MAC of ISO. The effects of DEX on HR and ventilation were similar in rats anaesthetized with HAL or ISO at 1 MAC; however, hypotension was more pronounced when DEX was combined with ISO at 1 MAC.     

Zinc(II), cadmium(II) and mercury(II) complexes of the vitamin B1 antagonist oxythiamine

The reaction of oxythiamine chloride hydrochloride (HOxTCl x HCl) with ZnCl2, CdCl2 and HgCl2 in ethanol yielded the complexes [ZnCl3(HOxT)], [CdCl3(HOxT)] and [HgCl3(HOxT)]. In water, the reaction with CdCl2 afforded [CdCl2(OxT)], but reaction with ZnCl2 or HgCl2 yielded unidentified products. The four new complexes were characterized by mass spectrometry and IR spectroscopy in the solid state and by 1H, 13C and 15N nuclear magnetic resonance (NMR) spectroscopy in hexadeuterated dimethylsulfoxide (DMSO-d6), and three were also studied by X-ray diffractometry. In [ZnCl3(HOxT)] and [HgCl3(HOxT)] the oxythiamine ligand is bound to the metal via N(1') and adopts the V conformation exhibited by thiamine in biological contexts. The infrared (IR) spectrum of [CdCl3(HOxT)] suggests a similar coordination mode. In [CdCl2(OxT)] each OxT zwitterion coordinates to one Cd(II) ion via its N(1') atom and to another via its N(3') and O atoms, giving rise to a polymeric chain along the x-axis. The coordination number of the metal is made up to six by Cdc...Cl interactions, two of which link the polymeric chains in pairs. This seems to be the first metal complex containing the oxythiamine ligand as a zwitterion, with the N(3')-H/O(4'alpha)-H group deprotonated. Neither HOxTCl nor its zinc(II) complex showed any significant activity in vitro against HeLa cells.     

Integrating Life Stages into Ecological Niche Models: A Case Study on Tiger Beetles

Detailed understanding of a species’ natural history and environmental needs across spatial scales is a primary requisite for effective conservation planning, particularly for species with complex life cycles in which different life stages occupy different niches and respond to the environment at different scales. However, niche models applied to conservation often neglect early life stages and are mostly performed at broad spatial scales. Using the endangered heath tiger beetle (Cicindela sylvatica) as a model species, we relate presence/absence and abundance data of locally dispersing adults and sedentary larvae to abiotic and biotic variables measured in a multiscale approach within the geographic extent relevant to active conservation management. At the scale of hundreds of meters, fine-grained abiotic conditions (i.e., vegetation structure) are fundamental determinants of the occurrence of both life stages, whereas the effect of biotic factors is mostly contained in the abiotic signature. The combination of dense heath vegetation and bare ground areas is thus the first requirement for the species’ preservation, provided that accessibility to the suitable habitat is ensured. At a smaller scale (centimetres), the influence of abiotic factors on larval occurrence becomes negligible, suggesting the existence of important additional variables acting within larval proximity. Sustained significant correlations between neighbouring larvae in the models provide an indication of the potential impact of neighbourhood crowding on the larval niche within a few centimetres. Since the species spends the majority of its life cycle in the larval stage, it is essential to consider the hierarchical abiotic and biotic processes affecting the larvae when designing practical conservation guidelines for the species. This underlines the necessity for a more critical evaluation of the consequences of disregarding niche variation between life stages when estimating niches and addressing effective conservation measures for species with complex life cycles.     

Factorial effects of salinity, dietary carbohydrate and moult cycle on digestive carbohydrases and hexokinases in Litopenaeus vannamei (Boone, 1931)

Litopenaeus vannamei were reared in close cycle over seven generations and tested for their capacity to digest starch and to metabolise glucose at different stages of the moulting cycle. After acclimation with 42.3% of carbohydrates (HCBH) or 2.3% carbohydrates (LCBH) diets and at high salinity (40 g kg(-1)) or low salinity (15 g kg(-1)), shrimp were sampled and hepatopancreas (HP) were stored. Total soluble protein in HP was affected by the interaction between salinity and moult stages (p<0.05). Specific activity of alpha-amylase ranged from 44 to 241 U mg protein(-1) and a significant interaction between salinity and moult stages was observed (p<0.05), resulting in highest values at stage C for low salinity (mean value 196.4 U mg protein(-1)), and at D0 in high salinity (mean value 175.7 U mg protein(-1)). Specific activity of alpha-glucosidase ranged between 0.09 and 0.63 U mg protein(-1), an interaction between dietary CBH and salinity was observed for the alpha-glucosidase (p<0.05) and highest mean value was found in low salinity-LCBH diet treatment (0.329 U mg protein(-1)). Hexokinase specific activity (range 9-113 mU mg protein(-1)) showed no significant differences when measured at 5 mM glucose (p>0.05). Total hexokinase specific activity (range 17-215 mU mg protein(-1)) showed a significant interaction between dietary CBH and salinity (p<0.05) with highest value (mean value 78.5 mU mg protein(-1)) found in HCBH-high salinity treatment, whereas in the other treatments the activity was not significantly different (mean value 35.93 mU mg protein(-1)). A synergistic effect of dietary CBH, salinity and moult stages over hexokinase IV-like specific activity was also observed (p<0.05). As result of this interaction, the highest value (135.5+/-81 mU mg protein(-1)) was observed in HCBH, high salinity at D0 moult stage. Digestive enzymes activity is enhanced in the presence of high starch diet (HCBH) and hexokinase can be induced at certain moulting stages under the influence of blood glucose level. Perspectives are opened to add more carbohydrates in a growing diet, exemplifying the potential approach for less-polluting feed.     

Forty years of carabid beetle research in Europe - from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation

‘Carabidologists do it all’ (Niemelä 1996a) is a phrase with which most European carabidologists are familiar. Indeed, during the last half a century, professional and amateur entomologists have contributed enormously to our understanding of the basic biology of carabid beetles. The success of the field is in no small part due to regular European Carabidologists’ Meetings, which started in 1969 in Wijster, the Netherlands, with the 14th meeting again held in the Netherlands in 2009, celebrating the 40th anniversary of the first meeting and 50 years of long-term research in the Dwingelderveld. This paper offers a subjective summary of some of the major developments in carabidology since the 1960s. Taxonomy of the family Carabidae is now reasonably established, and the application of modern taxonomic tools has brought up several surprises like elsewhere in the animal kingdom. Progress has been made on the ultimate and proximate factors of seasonality and timing of reproduction, which only exceptionally show non-seasonality. Triggers can be linked to evolutionary events and plausibly explained by the “taxon cycle” theory. Fairly little is still known about certain feeding preferences, including granivory and ants, as well as unique life history strategies, such as ectoparasitism and predation on higher taxa. The study of carabids has been instrumental in developing metapopulation theory (even if it was termed differently). Dispersal is one of the areas intensively studied, and results show an intricate interaction between walking and flying as the major mechanisms. The ecological study of carabids is still hampered by some unresolved questions about sampling and data evaluation. It is recognised that knowledge is uneven, especially concerning larvae and species in tropical areas. By their abundance and wide distribution, carabid beetles can be useful in population studies, bioindication, conservation biology and landscape ecology. Indeed, 40 years of carabidological research have provided so much data and insights, that among insects - and arguably most other terrestrial organisms - carabid beetles are one of the most worthwhile model groups for biological studies.     

ProtTest 3: fast selection of best-fit models of protein evolution

We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities. AVAILABILITY: ProtTest 3 source code and binaries are freely available under GNU license for download from http://darwin.uvigo.es/software/prottest3, linked to a Mercurial repository at Bitbucket (https://bitbucket.org/). CONTACT: dposada@uvigo.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Dispersal limitation and spatial scale affect model based projections of Pinus uncinata response to climate change in the Pyrenees

Species Distribution Models (SDMs) were employed to assess the potential impact of climate change on the distribution of Pinus uncinata in the Pyrenees, where it is the dominant tree species in subalpine forest and alpine tree lines. Predicting forest response to climate change is a challenging task in mountain regions but also a conservation priority. We examined the potential impact of spatial scale on SDM projections by conducting all analyses at four spatial resolutions. We further examined the potential effect of dispersal constraints by applying a threshold distance of maximal advancement derived from a spatially explicit, individual‐based simulation model of tree line dynamics. Under current conditions, SDMs including climatic factors related to stress or growth limitation performed best. These models were then employed to project P. uncinata distribution under two emission scenarios, using data generated from several regional climate models. At the end of this century, P. uncinata is expected to migrate northward and upward, occupying habitat currently inhabited by alpine plant species. However, consideration of dispersal limitation and/or changing the spatial resolution of the analysis modified the assessment of climate change impact on mountain ecosystems, especially in the case of estimates of colonization and extinction at the regional scale. Our study highlights the need to improve the characterization of biological processes within SDMs, as well as to consider simultaneously different scales when assessing potential habitat loss under future climate conditions.