Methods for differentiating prion types in food-producing animals

Prions are an enigma amongst infectious disease agents as they lack a genome yet confer specific pathologies thought to be dictated mainly, if not solely, by the conformation of the disease form of the prion protein (PrPSc). Prion diseases affect humans and animals, the latter including the food-producing ruminant species cattle, sheep, goats and deer. Importantly, it has been shown that the disease agent of bovine spongiform encephalopathy (BSE) is zoonotic, causing variant Creutzfeldt Jakob disease (vCJD) in humans. Current diagnostic tests can distinguish different prion types and in food- producing animals these focus on the differentiation of BSE from the non-zoonotic agents. Whilst BSE cases are now rare, atypical forms of both scrapie and BSE have been reported, as well as two types of chronic wasting disease (CWD) in cervids. Typing of animal prion isolates remains an important aspect of prion diagnosis and is now becoming more focused on identifying the range of prion types that are present in food-producing animals and also developing tests that can screen for emerging, novel prion diseases. Here, we review prion typing methodologies in light of current and emerging prion types in food-producing animals

The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology

1. Knowledge of species distribution is critical to ecological management and conservation biology. Effective management requires the detection of populations, which can sometimes be at low densities and is usually based on visual detection and counting. 2. Recently, there has been considerable interest in the detection of short species-specific environmental DNA (eDNA) fragments to allow aquatic species monitoring within different environments due to the potential of greater sensitivity over traditional survey methods which can be time-consuming and costly. 3. Environmental DNA analysis is increasingly being used in the detection of rare or invasive species and has also been applied to eDNA persistence studies and estimations of species biomass and distribution. When combined with next-generation sequencing methods, it has been demonstrated that entire faunas can be identified. 4. Different environments require different sampling methodologies, but there remain areas where laboratory methodologies could be standardized to allow results to be compared across studies. 5. Synthesis and applications. We review recently published studies that use eDNA to moni- tor aquatic populations, discuss the methodologies used and the application of eDNA analysis as a survey tool in ecology. We include innovative ideas for how eDNA can be used for conservation and management citing test cases, for instance, the potential for on-site analyses, including the application of eDNA analysis to carbon nanotube platforms or laser transmission spectroscopy to facilitate rapid on-site detections. The use of eDNA monitoring is already being adopted in the UK for ecological surveys

The application of eDNA for monitoring of the great crested newt in the UK

Current ecological surveys for great crested newts are time-consuming and expensive and can only be carried out within a short survey window. Additional survey methods which would facilitate the detection of rare or protected species such as the great crested newt (Triturus cristatus) would be extremely advanta- geous. Environmental DNA (eDNA) analysis has been utilized for the detection of great crested newts in Denmark. Here, the same methodology has been applied to water samples taken from UK ponds concurrently with conventional field surveying techniques. Our eDNA analysis exhibited an 84% success rate with a kappa coefficient of agreement between field and eDNA surveys of 0.86. One pond determined to be negative for great crested newt by field survey was positive by eDNA analysis, revealing the potential for improved detection rates using this methodology. Analysis of water samples collected in late summer indicates that eDNA analysis could be used to detect great crested newt after the optimal survey window for current field techniques had passed. Conse- quently, eDNA analysis could augment currently stipulated techniques for great crested newt surveying as a relatively quick and inexpensive tool for collecting great crested newt presence and distribution data within the UK instead of or prior to full field surveys

Electrochemical and Structural Characterization of Azotobacter vinelandii Flavodoxin II

Azotobacter vinelandii flavodoxin II serves as a physiological reductant of nitrogenase, the enzyme system mediating biological nitrogen fixation. Wildtype A. vinelandii flavodoxin II was electrochemically and crystallographically characterized to better understand the molecular basis for this functional role. The redox properties were monitored on surfactant-modified basal plane graphite electrodes, with two distinct redox couples measured by cyclic voltammetry corresponding to reduction potentials of −483 ± 1 mV and −187 ± 9 mV (vs. NHE) in 50 mM potassium phosphate, 150 mM NaCl, pH 7.5. These redox potentials were assigned as the semiquinone/hydroquinone couple and the quinone/semiquinone couple, respectively. This study constitutes one of the first applications of surfactant-modified basal plane graphite electrodes to characterize the redox properties of a flavodoxin, thus providing a novel electrochemical method to study this class of protein. The X-ray crystal structure of the flavodoxin purified from A. vinelandii was solved at 1.17 Å resolution. With this structure, the native nitrogenase electron transfer proteins have all been structurally characterized. Docking studies indicate that a common binding site surrounding the Fe-protein [4Fe:4S] cluster mediates complex formation with the redox partners Mo-Fe protein, ferredoxin I, and flavodoxin II. This model supports a mechanistic hypothesis that electron transfer reactions between the Fe-protein and its redox partners are mutually exclusive

The application of eDNA for monitoring of the great crested newt in the UK

Current ecological surveys for great crested newts are time-consuming and expensive and can only be carried out within a short survey window. Additional survey methods which would facilitate the detection of rare or protected species such as the great crested newt (Triturus cristatus) would be extremely advanta- geous. Environmental DNA (eDNA) analysis has been utilized for the detection of great crested newts in Denmark. Here, the same methodology has been applied to water samples taken from UK ponds concurrently with conventional field surveying techniques. Our eDNA analysis exhibited an 84% success rate with a kappa coefficient of agreement between field and eDNA surveys of 0.86. One pond determined to be negative for great crested newt by field survey was positive by eDNA analysis, revealing the potential for improved detection rates using this methodology. Analysis of water samples collected in late summer indicates that eDNA analysis could be used to detect great crested newt after the optimal survey window for current field techniques had passed. Conse- quently, eDNA analysis could augment currently stipulated techniques for great crested newt surveying as a relatively quick and inexpensive tool for collecting great crested newt presence and distribution data within the UK instead of or prior to full field surveys

A survey in natural forest ecosystems of Vietnam reveals high diversity of both new and described Phytophthora taxa including P. ramorum

In 2016 and 2017, surveys of Phytophthora diversity were performed in 25 natural and semi-natural forest stands and 16 rivers in temperate and subtropical montane and tropical lowland regions of Vietnam. Using baiting assays from soil samples and rivers and direct isolations from naturally fallen leaves, 13 described species, five informally designated taxa and 21 previously unknown taxa of Phytophthora were isolated from 58 of the 91 soil samples (63.7%) taken from the rhizosphere of 52 of the 64 woody plant species sampled (81.3%) in 20 forest stands (83.7%), and from all rivers: P. capensis, P. citricola VII, VIII, IX, X and XI, P. sp. botryosa-like 2, P. sp. meadii-like 1 and 2, P. sp. tropicalis-like 2 and P. sp. multivesiculata-like 1 from Phytophthora major phylogenetic Clade 2; P. castaneae and P. heveae from Clade 5; P. chlamydospora, P. gregata, P. sp. bitahaiensis-like and P. sp. sylvatica-like 1, 2 and 3 from Clade 6; P. cinnamomi (Pc), P. parvispora, P. attenuata, P. sp. attenuata-like 1, 2 and 3 and P. ×heterohybrida from Clade 7; P. drechsleri, P. pseudocryptogea, P. ramorum (Pr) and P. sp. kelmania from Clade 8, P. macrochlamydospora, P. sp. ×insolita-like, P. sp. ×kunnunara-like, P. sp. ×virginiana-like s.l. and three new taxa, P. sp. quininea-like, P. sp. ×Grenada 3-like and P. sp. ×Peru 4-like, from Clade 9; and P. sp. gallica-like 1 and 2 from Clade 10. The A1 and A2 mating types of both Pc and Pr co-occurred. The A2 mating type of Pc was associated with severe dieback of montane forests in northern Vietnam. Most other Phytophthora species, including Pr, were not associated with obvious disease symptoms. It is concluded that (1) Vietnam is within the center of origin of most Phytophthora taxa found including Pc and Pr, and (2) Phytophthora clades 2, 5, 6, 7, 8, 9, and 10 are native to Indochina.info:eu-repo/semantics/publishedVersio

アトガキ

ObjectiveAnalysis of environmental DNA (eDNA) is a method that has been used for the detection of various species within water bodies. The great crested newt (Triturus cristatus) has a short eDNA survey season (mid-April to June). Here we investigate whether this season could be extended into other months using the current methodology as stipulated by Natural England.ResultsHere we present data to show that in monthly water samples taken from two ponds (March 2014–February 2015) we were able to detect great crested newt DNA in all months in at least one of the ponds. Similar levels of great crested newt eDNA (i.e. highly positive identification) were detected through the months of March–August, suggesting it may be possible to extend the current survey window. In order to determine how applicable these observations are for ponds throughout the rest of the UK, further work in multiple other ponds over multiple seasons is suggested. Nevertheless, the current work clearly demonstrates, in two ponds, the efficacy and reproducibility of eDNA detection for determining the presence of great crested newts

Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian

Background: Environmental DNA (eDNA) metabarcoding is revolutionizing biodiversity monitoring, but has unrealized potential for ecological hypothesis generation and testing. Aims: Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. Materials & Methods: We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T.cristatus detection at the pondscape. Furthermore, we test the status of T.cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T.cristatus and higher T.cristatus Habitat Suitability Index (HSI) scores. Results: Triturus cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T.cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). Triturus cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus), and ninespine stickleback (Pungitius pungitius) were identified. Triturus cristatus detection was negatively correlated with mammal species richness, and T.cristatus was negatively associated with gray squirrel (Sciurus carolinensis). Triturus cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T.cristatus survey. Vertebrate species richness was significantly higher in T.cristatus ponds and broadly increased as T.cristatus HSI scores increased. Discussion: We reaffirm reported associations (e.g., T.cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T.cristatus. Conclusion: Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring, and research

Referral pathways for TIA patients avoiding hospital admission : a scoping review

Objective: To identify the features and effects of a pathway for emergency assessment and referral of patients with suspected transient ischaemic attack (TIA) in order to avoid admission to hospital.Design: Scoping review.Data sources: PubMed, CINAHL Web of Science, Scopus.Study selection: Reports of primary research on referral of patients with suspected TIA directly to specialist outpatient services.Data extraction: We screened studies for eligibility and extracted data from relevant studies. Data were analysed to describe setting, assessment and referral processes, treatment, implementation and outcomes.Results: 8 international studies were identified, mostly cohort designs. 4 pathways were used by family doctors and 3 pathways by emergency department physicians. No pathways used by paramedics were found. Referrals were made to specialist clinic either directly or via a 24-hour helpline. Practitioners identified TIA symptoms and risk of further events using a checklist including the ABCD2 tool or clinical assessment. Antiplatelet medication was often given, usually aspirin unless contraindicated. Some patients underwent tests before referral and discharge. 5 studies reported reduced incident of stroke at 90 days, from 6–10% predicted rate to 1.3–2.1% actual rate. Between 44% and 83% of suspected TIA cases in these studies were referred through the pathways.Conclusions: Research literature has focused on assessment and referral by family doctors and ED physicians to reduce hospitalisation of patients with TIA. No pathways for paramedical use were reported. We will use results of this scoping review to inform development of a paramedical referral pathway to be tested in a feasibility trial

Continued High Risk Sexual Behavior Following Diagnosis with Acute HIV Infection in South Africa and Malawi: Implications for Prevention

Understanding sexual behavior following diagnosis of acute HIV infection (AHI) is key to developing prevention programs targeting individuals diagnosed with AHI. We conducted separate qualitative and quantitative interviews with individuals newly diagnosed (n = 19) with AHI at 1-, 4- and 12-weeks post-diagnosis and one qualitative interview with individuals who had previously been diagnosed with AHI (n = 18) in Lilongwe, Malawi and Johannesburg, South Africa between October 2007 and June 2008. The majority of participants reported engaging in sexual activity following diagnosis with AHI with a significant minority reporting unprotected sex during this time. Most participants perceived to have changed their behavior following diagnosis. However, participants reported barriers to condom use and abstinence, in particular, long term relationships and the need for disclosure of sero-status. Understanding of increased infectiousness during AHI was limited. Participants reported a desire for a behavioral intervention at the time of AHI diagnosis, however, there were differences by country in the types of interventions participants found acceptable. Studies are underway to determine the feasibility, acceptability and potential effectiveness of interventions designed for individuals with AHI