Isolation of Psoroptes scab mite microsatellite markers (Acari: Psoroptidae)

Nine microsatellite markers have been isolated from the scab mite,Psoroptes ovis. These markers have been tested for polymorphism in individual Psoroptes mites originating from two hosts, the European rabbit, Oryctolagus cuniculus, and sheep, Ovis aries. No definitive picture of Psoroptes species’ status or interrelationships exists. This study provides the basis for a new molecular system to elucidate the systematics of groupings within the genus Psoroptes, allowing us to clarify the population dynamics and epidemiology of the mites causing sheep scab world wide

Screening of cryptic species among clinical Aspergillus isolates collected during one year period in a Portuguese reference laboratory

Objectives: Correct identification of Aspergillus species is important given that sibling species may show variable susceptibilities to multiple antifungal drugs and also because sharper definition of species may facilitate epidemiological studies. Thus, we screened Aspergillus clinical isolates from Portuguese hospitals to determine which, if any, of the cryptic species of Aspergillus were involved in patient infections. Methods: Over a one year period, Aspergillus isolates from Portuguese health institutions were collected. These isolates were identified on the basis of microscopic morphology and through the use of molecular tools. Genomic DNA was prepared from each isolate and the sequencing of the Internal Transcribed Spacers (ITS) regions, specifically the ITS1 and ITS2 non-coding regions flanking the 5.8S rDNA was used to determine the species complex, whereas β-tubulin and calmodulin sequencing was done to achieve the correct species identification. Results: Over the study period, 57 Aspergillus isolates from clinical samples were collected from 10 Portuguese health institutions. According to the morphological observations, 29 isolates were identified as Aspergillus fumigatus, 11 A. flavus, 8 A. niger, 3 A. nidulans, 2 A. terreus, 2 A. candidus and 2 Aspergillus sp. Among those isolates, six species-complexes were detected by ITS sequencing, and were distributed as follows: fumigati (50.1%), flavi (21.0%), nigri (15.8%), terrei (5.3%), nidulantes (3.6%) and versicolores (3.6%). β-tubulin and calmodulin sequencing resulted in ten (17.5%) cryptic species being identified among the 57 isolates. Six of those isolates belonged to the nigri complex (A. brasiliensis, A. awamorii and A. tubigensis), two to the versicolores complex (A. sidowii and A. fructus), one to the fumigati complex (A. lentulus) and one to the nidulantes complex (Emmericella echinulata). Conclusion: With rigorous application of molecular tools, cryptic species of Aspergillus are not uncommon in the clinic. The identification of cryptic species among the collected clinical isolates of Aspergillus alerts the clinician to isolates with reduced susceptibilities to antifungal drugs and emphasizes a correct identification to species level

Surveillance of environmental fungi, with focus on Aspergillus, in a Portuguese Central Hospital.

Objectives: Because immunocompromised patients are more prone to acquire nosocomial infections caused by fungi isolated from the environment, e.g. Aspergillus, this study aimed to screen the hospital environment for the presence of fungi and to understand their epidemiology in the different hospital wards analyzed. Methods: During one-year period, four seasonal samplings, i.e., air and hard surface, were performed. A total of 101 air samples and 99 surface samples were collected from the Hematology, Oncology, and Intensive Care Unit (ICU) wards of a Portuguese Central Hospital. Aspergillus isolates were plated for growth as single colonies on malt extract agar with chloramphenicol to check the colony purity and observe colonial morphology. The universal fungal primers ITS1 and ITS4 were used to amplify DNA from all Aspergillus isolates, amplimers were sequenced, and isolates identified to the species-complex level. Statistical analyses were done using SPSS v15.0 program for Windows. Results: Aspergillus was the most frequently recovered fungal genus (20.9%), followed by Cladosporium (18.7%), and Penicillium (17.2%). Thirty-five Aspergillus isolates were collected from the wards with hematological patients (bone marrow transplant and hemato-oncology wards), whereas 15 isolates were recovered from ICU. Among Aspergillus isolates from the hospital environment, those belonging to the species-complexes of versicolores (n = 26; 32.5%), nigri (n = 12; 15.0%), flavi (n = 11; 13.7%), and circumdati (n = 6; 7.5%) dominated. Hemato-Oncology was the ward with higher fungal counts, whereas the bone marrow transplant ward, which is protected by HEPA-filtration of the supply air, showed the lowest numbers in all sampling periods. A significant association (p = 0.001) was found between the season and the Aspergillus complexes isolated, with spring and summer having a larger number of different species-complexes detected in the hospital´s air and on the surfaces. Nevertheless, air counts showed that the autumn was the season with the highest proportion of Aspergillus (one third of the total number of fungi detected). This could be due in part to the presence of construction work near these wards. Conclusion: The knowledge of the epidemiology of environmental fungi in each hospital may allow the establishment of preventive or corrective measures to decrease nosocomial fungal infections

A framework for realistic 3D tele-immersion

Meeting, socializing and conversing online with a group of people using teleconferencing systems is still quite differ- ent from the experience of meeting face to face. We are abruptly aware that we are online and that the people we are engaging with are not in close proximity. Analogous to how talking on the telephone does not replicate the experi- ence of talking in person. Several causes for these differences have been identified and we propose inspiring and innova- tive solutions to these hurdles in attempt to provide a more realistic, believable and engaging online conversational expe- rience. We present the distributed and scalable framework REVERIE that provides a balanced mix of these solutions. Applications build on top of the REVERIE framework will be able to provide interactive, immersive, photo-realistic ex- periences to a multitude of users that for them will feel much more similar to having face to face meetings than the expe- rience offered by conventional teleconferencing systems

Identification of Aspergillus cryptic species in hospital environment

Selected hospital wards, housing patients at higher risk to develop invasive fungal infections, were screened in order to understand the epidemiology and distribution of Aspergillus, especially regarding the presence of cryptic species.Aspergillus species were identified by b-tubulin and calmodulin sequencing, and a high percentage of cryptic species (i.e., not sensu stricto) was found (59%). Sections Usti, Versicolores and Circumdati harbored the highest proportion of cryptic species [100% (4/4), 95% (19/20) and 90% (9/10), respectively].The high number of cryptic species found raises concerns about the possible reduced susceptibility to antifungals of hospital environmental Aspergillus isolates. These data reinforce the importance of hospital air and surface monitoring, mainly in immunocompromised patients’ wards

A Simple Game-Theoretic Approach to Checkonly QVT Relations

The QVT Relations (QVT-R) transformation language allows the def-inition of bidirectional model transformations, which are required in cases where a two (or more) models must be kept consistent in the face of changes to either. A QVT-R transformation can be used either in check-only mode, to determine whether a target model is consistent with a given source model, or in enforce mode, to change the target model. Al-though the most obvious semantic issues in the QVT standard concern the restoration of consistency, in fact even checkonly mode is not completely straightforward; this mode is the focus of this paper. We need to consider the overall structure of the transformation as given by when and where clauses, and the role of trace classes. In the standard, the semantics of QVT-R are given both directly, and by means of a translation to QVT Core, a language which is intended to be simpler. In this paper, we argue that there are irreconcilable differences between the intended semantics of QVT-R and those of QVT Core, so that the translation cannot be helpful. Treating QVT-R directly, we propose a simple game-theoretic semantics. We demonstrate its behaviour on examples and show how it can be used to compare QVT-R transformations. We demonstrate that consistent models may not possess a single trace model whose objects can be read as traceability links in either direction. We briefly discuss the ef-fect of variations in the rules of the game, to elucidate some design choices available to the designers of the QVT-R language.

Bovine tuberculosis in Northern Ireland : risk factors associated with time from post-outbreak test to subsequent herd breakdown

Compulsory bovine tuberculosis testing has been implemented since 1959 in NorthernIreland. Initial rapid progress in the eradication of the disease was followed by a situationwhere disease levels tended to fluctuate around a low level. This study explores recru-descence of bovine tuberculosis (bTB) in Northern Ireland herds by assessing risk factorsassociated with time from the six-month post-outbreak skin test until a further herd break-down. Bovine herds (n = 3377) were recruited in 2002 and 2003 and their survival analysedusing Kaplan–Meier survival estimates and a Cox proportional hazards model, with follow-up extending to August 2008. Exclusion criteria applied for study entry were bTB infection ina contiguous herd, changing of post restriction test to one of a higher risk status or chronicinfection. Chronic infection was defined as any situation where disclosure preceded thepost-outbreak test by two years or more. The application of these exclusion criteria meantthat herds recruited to the study were largely cleared of infection and not directly con-tiguous to other infected herds. Of the 3377 herds, 1402 (41.5%) suffered a further herdbreakdown before the end of follow-up. Median survival time was 582 days (interquartilerange = 336–1002 days). Breakdown severity (defined as the number of Single Intrader-mal Comparative Tuberculin Test (SICTT) reactors at disclosure test), local bTB prevalence,herd size and type were identified as significant risk factors (p 27.38 per year) of cattle. Consistent with other studies this workshows bTB confirmation to not be predictive of a future herd breakdown. This work showsbTB history as not being a risk factor for a future breakdown. This result could be reflectiveof the exclusion criteria used in the study, which may have selected for incidents wherehistorical status was of less importance.http://www.elsevier.com/locate/prevetmedhb201

The use of different 16S rRNA gene variable regions in biogeographical studies.

16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.Gilda Varliero, Pedro H. Lebre, Mark I. Stevens, Paul Czechowski, Thulani Makhalanyane, Don A. Cowa