Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

BACKGROUND

Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.

RESULTS

Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.

CONCLUSIONS

Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

Do small barriers affect the movement of freshwater fish by increasing residency?

River fragmentation due to artificial barriers directly impacts fish communities by limiting migratory movements. This work aims to understand how small barriers affect the movements of a potamodromous cyprinid species - the Iberian barbel (Luciobarbus bocagei (Steindachner, 1864)) - in a 5.6km upstream segment of a stream impacted only by the presence of physical barriers. Fish were marked with Visible Implant Elastomer tags (VIE), and barriers were seasonally characterized. A total of 683 fish were tagged, with 104 recaptures, during five sampling seasons (spring 2012 - early summer 2013). Eleven of the recaptured fish moved past a barrier, without any preference in terms of direction of movement. There were no differences in length, either between migrants and residents, or between upstream and downstream migrants. The results show that although barbel are able to negotiate small barriers, part of the population did not move between fragmented reaches - an indication that under such conditions, fish species populations may adjust their life-history strategy to augment residency as it was hypothesized from the results.

Potamodromous fish movements under multiple stressors: Connectivity reduction and oxygen depletion

Rivers are impacted by multiple stressors that can interact to create synergistic, additive or antagonistic effects, but experimental studies on fish encompassing more than one stressor are seldom found. Thus, there is the need to study stressors through multifactorial approaches that analyse the impact of fish exposure to multiple stressors and evaluate fish sensitivity to stressor combinations. Some of the most common impacts to Mediterranean rivers are of two natures: i) water abstraction and ii) diffuse pollution. Therefore, the present study aims at studying the responses of potamodromous fish facing combinations of: 1) a primary stressor (two levels of connectivity reduction due to water scarcity), and 2) a secondary stressor (three levels of oxygen depletion due to increase organic load - of anthropogenic nature). Schools of five wild fish from a cyprinid species (Luciobarbus bocagei) were placed in a flume, equipped with see-through sidewalls to allow for behavioural analysis, and subjected to different combinations of the stressors. Results show that at the unconnected level the primary stressor (lack of connectivity) overrode the effect of the secondary stressor (oxygen depletion), but when connectivity existed oxygen depletion caused a reduction of fish movements with decreasing oxygen concentrations. This multifactorial study contributes to improved prediction of fish responses upon actual or projected pressure scenarios.

Cell shape dynamics during the staphylococcal cell cycle

Staphylococcus aureus is an aggressive pathogen and a model organism to study cell division in sequential orthogonal planes in spherical bacteria. However, the small size of staphylococcal cells has impaired analysis of changes in morphology during the cell cycle. Here we use super-resolution microscopy and determine that S. aureus cells are not spherical throughout the cell cycle, but elongate during specific time windows, through peptidoglycan synthesis and remodelling. Both peptidoglycan hydrolysis and turgor pressure are required during division for reshaping the flat division septum into a curved surface. In this process, the septum generates less than one hemisphere of each daughter cell, a trait we show is common to other cocci. Therefore, cell surface scars of previous divisions do not divide the cells in quadrants, generating asymmetry in the daughter cells. Our results introduce a need to reassess the models for division plane selection in cocci.

Staphylococci are spherical bacteria that divide in sequential orthogonal planes. Here, the authors use super-resolution microscopy to show that staphylococcal cells elongate before dividing, and that the division septum generates less than one hemisphere of each daughter cell, generating asymmetry.

Riparian buffer zones as pesticide filters of no-till crops

Several studies have pointed to the potential benefits of riparian vegetation as buffer zones for agricultural and industrial pollutants harmful to aquatic ecosystems. However, other studies have called into question its use as an ecological filter, questioning the widths and conditions for which they are effective as a filter. In this work, we have investigated the buffering capacity of the riparian one to retain pesticides in the water-saturated zone, on 27 sites composed by riparian buffer zones with different vegetation structure (woody, shrubs, or grass vegetation) and width (12, 36, and 60 m). Five pesticides were analyzed. The effectiveness of the filtering was largely influenced by the width and vegetation type of the buffer zone. In general, decreasing pesticide removal followed in this order wood > shrubs > grass. The 60 m woody buffer zone was the most effective in the removal of all the pesticides. Only atrazine was detected in this case (0.3 μg L(-1)). Furthermore, a linear correlation (R (2) > 0.97) was observed in their removal for all compounds and buffer zones studied. Thus, preserving the woody vegetation in the riparian zone is important for watershed management and groundwater quality in the no-tillage system in temperate climate.

Potential distribution and cost estimation of the damage caused by Cryptotermes brevis (Isoptera: Kalotermitidae) in the Azores

In the Azores archipelago, a significant proportion of buildings are infested with the urban exotic drywood termite Cryptotermes brevis (Walker), causing major economical and patrimonial losses. This work aims to understand the potential spread of this termite species in the Azores and estimate the costs for both treatment and reconstruction of infested buildings in the entire archipelago. A maximum entropy niche modeling process was used to determine the potential occurrence of the species on each island. Different scenarios were built using independent global and regional incidence and environmental data. Both projections reveal the same pattern. Generally, the probability of occurrence is higher near the coast line, where, in Azores, the majority of the towns and villages are located. We also predict that the infestation has potential to spread to yet unaffected towns and islands. It is estimated that the cost of treating all currently infested buildings in the archipelago is Euro 51 million, while reconstruction of the same buildings would rise the costs to Euro 175 million. We predict that the absence of a control strategy will cause a further expansion of the pest to more localities in the Azores. An estimate to future scenarios implies higher costs, with treatment and rebuilding values rising up to eight times the current values.

Comparability of fish-based ecological quality assessments for geographically distinct Iberian regions

In this work we compare two Iberian and a pan-European fish-based methods to assess ecological quality in rivers: the Fish-based Index of Biotic Integrity for Portuguese Wadeable Streams (F-IBIP), the Mediterranean Index of Biotic Integrity (IBIMED) and the pan-European Fish Index (EFI+). The results presented herein were developed in the context of the 2nd phase of the Intercalibration Exercise (IC), as required by the Water Frame Directive (WFD). The IC is aimed at ensuring comparability of the quality boundaries among the different WFD assessment methods developed by the Member States for each biological quality element. Although the two national assessment methods were developed for very distinct regions of Iberia (Western and Eastern Iberian Peninsula) they share the same methodological background: both are type-specific and guild-based multimetric indices. EFI+ is a multimetric guild-based model, but it is site-specific and uses a predictive modelling approach. The three indices were computed for all sites included in the Iberian Intercalibration database to allow the direct comparison, by means of linear regressions, of the resulting three quality values per site. The quality boundary harmonization between the two Iberian methods was only possible through an indirect comparison between the two indices, using EFI+ as a common metric. The three indices were also shown to be responsive to a common set of human induced pressures. This study highlights the need to develop general assessment methods adapted to wide geographical ranges with high species turnover to help intercalibrating assessment methods tailored for geographically more restricted regions.

Least Disturbed Condition for European Mediterranean rivers

The present report describes a three-step approach that was used to characterize and define thresholds for the Least Disturbed Condition in Mediterranean streams of four different types, regarding organic pollution and nutrients, hydrological and morphological alterations, and land use. For this purpose, a common database composed of national reference sites (929 records) from seven countries, sampled for invertebrates, diatoms and macrophytes was used. The analyses of reference sites showed that small (catchment <100 km(2)) siliceous and non-siliceous streams were mainly affected by channelization, bank alteration and hydropeaking. Medium-sized siliceous rivers were the most affected by stressors: 25-43% of the samples showed at least slight alterations regarding channelization, connectivity, upstream dam influence, hydropeaking and degradation of riparian vegetation. Temporary streams were the least affected by hydromorphological changes, but they were nevertheless affected by alterations in riparian vegetation. There were no major differences between all permanent stream types regarding water quality, but temporary streams showed lower values for oxygenation (DO) and wider ranges for other variables, such as nitrates. A lower threshold value for DO (60%) was determined for this stream type and can be attributed to the streams' natural characteristics. For all other river types, common limits were found for the remaining variables (ammonium, nitrate, phosphate, total P, % of artificial areas, % of intensive and extensive agriculture, % of semi-natural areas in the catchment). These values were then used to select the list of reference sites. The biological communities were characterized, revealing the existence of nine groups of Mediterranean invertebrate communities, six for diatoms and five for macrophytes: each group was characterized by specific indicator taxa that highlighted the differences between groups.

Comparability of river quality assessment using macrophytes: a multi-step procedure to overcome biogeographical differences

This paper exposes a new methodological approach to solve the problem of intercalibrating river quality national methods when a common metric is lacking and most of the countries share the same Water Framework Directive (WFD) assessment method. We provide recommendations for similar works in future concerning the assessment of ecological accuracy and highlight the importance of a good common ground to make feasible the scientific work beyond the intercalibration. The approach herein presented was applied to highly seasonal rivers of the Mediterranean Geographical Intercalibration Group for the Biological Quality Element Macrophytes. The Mediterranean Group of river macrophytes involved seven countries and two assessment methods with similar acquisition data and assessment concept: the Macrophyte Biological Index for Rivers (IBMR) for Cyprus, France, Greece, Italy, Portugal and Spain, and the River Macrophyte Index (RMI) for Slovenia. Database included 318 sites of which 78 were considered as benchmarks. The boundary harmonization was performed for common WFD-assessment methods (all countries except Slovenia) using the median of the Good/Moderate and High/Good boundaries of all countries. Then, whenever possible, the Slovenian method, RMI was computed for the entire database. The IBMR was also computed for the Slovenian sites and was regressed against RMI in order to check the relatedness of methods (R(2)=0.45; p<0.00001) and to convert RMI boundaries into the IBMR scale. The boundary bias of RMI was computed using direct comparison of classification and the median boundary values following boundary harmonization. The average absolute class differences after harmonization is 26% and the percentage of classifications differing by half of a quality class is also small (16.4%). This multi-step approach to the intercalibration was endorsed by the WFD Regulatory Committee.

Cryptotermes brevis (Isoptera: Kalotermitidae) in the Azores: lessons after 2 yr of monitoring in the Archipelago

The dispersal flights of West Indian drywood termite, Cryptotermes brevis (Walker) (Isoptera: Kalotermitidae) were surveyed in the major cities of Azores. The sampling device used to estimate termite density consisted of a yellow adhesive trap (size 45 by 24 cm), placed with an artificial or natural light source in a dark attic environment. In addition, data from two other projects were used to improve the knowledge about the geographical distribution of the species. The level of infestation in the two main Azorean towns differed, with high levels in the houses of Angra do Heroísmo, whereas in Ponta Delgada, there are fewer houses with high levels of infestation. The infestation in Ponta Delgada shows a pattern of spreading from the center outward to the city's periphery, whereas in Angra do Heroísmo, there was a pattern of spreading outward from several foci. The heavy infestation observed in Angra do Heroísmo and the clear increase of infestation levels observed from 2010 to 2011 is a reason for concern and calls for an urgent application of an Integrated Pest Management (IPM) control strategy.

Pool-type fishways: two different morpho-ecological cyprinid species facing plunging and streaming flows

Fish are particularly sensitive to connectivity loss as their ability to reach spawning grounds is seriously affected. The most common way to circumvent a barrier to longitudinal connectivity, and to mitigate its impacts, is to implement a fish passage device. However, these structures are often non-effective for species with different morphological and ecological characteristics so there is a need to determine optimum dimensioning values and hydraulic parameters. The aim of this work is to study the behaviour and performance of two species with different ecological characteristics (Iberian barbel Luciobarbus bocagei-bottom oriented, and Iberian chub Squalius pyrenaicus-water column) in a full-scale experimental pool-type fishway that offers two different flow regimes-plunging and streaming. Results showed that both species passed through the surface notch more readily during streaming flow than during plunging flow. The surface oriented species used the surface notch more readily in streaming flow, and both species were more successful in moving upstream in streaming flow than in plunging flow. Streaming flow enhances upstream movement of both species, and seems the most suitable for fishways in river systems where a wide range of fish morpho-ecological traits are found.

Attraction of alates of Cryptotermes brevis (Isoptera: Kalotermitidae) to different light wavelengths in South Florida and the Azores

The termite Cryptotermes brevis (Walker) (Isoptera: Kalotermitidae) is an urban pest that causes much damage to wood structures. Little has been done concerning the use of control methods for alates. C. brevis is known to have phototropic behavior during the dispersal flights, and this knowledge has been applied for preventative control in the Azores where this species is a serious urban pest. We were interested in determining whether there was a light wavelength preference by the alates of C. brevis to optimize light traps against this species. Six light wavelengths were tested: 395 nm (UV), 460-555 nm (white), 470 nm (blue), 525 nm (green), 590 nm (yellow), and 625 nm (red) in choice chambers, with dark chambers as controls. Two populations were tested, one population in Florida and one population in the Azores (Terceira Island). We found consistent results for both populations, with a preference for the light wavelengths in the white, blue, and green spectrum (460-550 nm). This information can be used to build more effective light traps that can be used by home owners in the Azores to help control this pest.

Modelling stream-fish functional traits in reference conditions: regional and local environmental correlates

Identifying the environmental gradients that control the functional structure of biological assemblages in reference conditions is fundamental to help river management and predict the consequences of anthropogenic stressors. Fish metrics (density of ecological guilds, and species richness) from 117 least disturbed stream reaches in several western Iberia river basins were modelled with generalized linear models in order to investigate the importance of regional- and local-scale abiotic gradients to variation in functional structure of fish assemblages. Functional patterns were primarily associated with regional features, such as catchment elevation and slope, rainfall, and drainage area. Spatial variations of fish guilds were thus associated with broad geographic gradients, showing (1) pronounced latitudinal patterns, affected mainly by climatic factors and topography, or (2) at the basin level, strong upstream-downstream patterns related to stream position in the longitudinal gradient. Maximum native species richness was observed in midsize streams in accordance with the river continuum concept. The findings of our study emphasized the need to use a multi-scale approach in order to fully assess the factors that govern the functional organization of biotic assemblages in ‘natural’ streams, as well as to improve biomonitoring and restoration of fluvial ecosystems.

[Pain: its occurrence and evolution in the postoperative period of heart and abdominal surgery]

The high incidence and low resolution of the pain after surgery are shown in international literature. During the five days after the cardiac and abdominal surgery, these patients were asked once a day about their pain. Nearly 50% of the patients answers showed pain complaints. At the cardiac patients 47% did not take treatment during the last four hours, although the medicine was prescribed by the doctor to be used in eventual necessity. Similar occurrences happened with abdominal patients where no medicine was given in 68.2% events of their pain complaints. So, we find that the under-identification and undertreatment of the pain are like the other studies.

Portuguese patients as part of the canadian mosaic

Portuguese immigration is a relatively new addition to the Canadian ethnic mosaic. To help the Canadian family doctor become familiar with this new group, the experience of a predominantly Portuguese family practice is described. The main areas of concern centre around the working wife, the problems created by the uprooting of old people and the adaptation of the children to this new environment. Some conflicts created in the family by the new situation are described and solutions suggested.