E. J. McLuckie to James Meredith (2 October 1962)

https://egrove.olemiss.edu/mercorr_pro/1879/thumbnail.jp

Novel single nucleotide polymorphism-based assay for genotyping Mycobacterium avium subsp. paratuberculosis

Typing of Mycobacterium avium subspecies paratuberculosis strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of Mycobacterium avium subspecies paratuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133 Mycobacterium avium subspecies paratuberculosis isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs Mycobacterium avium subspecies paratuberculosis isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit–variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of Mycobacterium avium subspecies paratuberculosis isolates

A post-mortem study of respiratory disease in small mustelids in south-west England

14 páginas, 3 tablas, 11 figuras.--This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: Stoat (Mustela erminea) and weasel (Mustela nivalis) populations in south-west England are declining whilst polecats (Mustela putorius), absent for over a century, are increasing. Little is known about the health status of these species nationally. This study aimed at investigating respiratory disease in specimens found dead in south-west England. Results: Trauma caused by road traffic, predator attack or being trapped was the predominant cause of death in 42 stoats, 31 weasels and 20 polecats; most were in good physical condition. Skrjabingylus nasicola was present in all species (weasels 37 %, polecats 39 %, stoats 41 %) and infected animals showed no evidence of loss of body condition. Even in carcases stored frozen L larvae were frequently alive and highly motile. Angiostrongylus vasorum infection was diagnosed in two stoats and one weasel: in stoats infections were patent and the lung lesions were likely of clinical significance. These are believed to be the first records of A. vasorum in small mustelids. Pleuritis and pyothorax was seen in two polecats, in one case due to a migrating grass awn. Histological examination of lungs showed granulomata in stoats (38 %), weasels (52 %) and polecats (50 %). Spherules consistent with Emmonsia spp. adiaspores were present in the granulomata of stoats (60 %), weasels (36 %) and polecats (29 %). Adiaspore diameter in all three species was similar (means: stoats 39 μm, weasels 30 μm, polecats 36 μm); these are markedly smaller than that normally recorded for E. crescens. Although they lie within the accepted range for spores of Emmonsia parva this arid-zone species is not found in Britain, thus raising a question over the identity of the fungus. Cases showing numerous granulomata but few or no adiaspores were Ziehl-Neelsen-stain negative for acid-fast bacilli and IHC negative for Mycobacterium spp. However, in some cases PCR analyses revealed mycobacteria, including Mycobacterium kumamotonense and Mycobacterium avium Complex. One stoat had numerous unidentified small organisms present centrally within granulomata. Conclusions: Stoats, weasels and polecats in south-west England share several respiratory diseases, often of high prevalence, but the pathology would appear insufficient to impact on the health status of the populations and other ultimate causes of death should be investigated when examining these species.The authors gratefully acknowledge the histological support given by Trevor Whitbread, Judith Hargreaves, Richard Fox, Lucy Oldroyd, Malcolm Silkstone, Sonja Rivers and Michelle Woodman at Abbey Veterinary Services. They also thank Nicholas Davison, Beverley Rule and Philip Booth, AHVLA Truro, Mark Wessels, Finn Pathologists, Luke Roberts and Eric Morgan, Bristol University, Marc Artois, Campus Vétérinaire de Lyon. Becki Lawson, Fieke Molenaar, Tamsyn Stephenson, Zoe Greatorex and Jane Simpson at Wildlife Veterinary Investigation Centre assisted with post-mortem-examinations. David Groves, Kate Stokes, Derek Lord and Cornwall Mammal Group and Cornwall Wildlife Trust members and staff, James Williams, Somerset Otter Group, and David Couper, Royal Society for the Prevention of Cruelty to Animals helped with carcase submissions. Andrew Borman, Mycology Reference Laboratory South West Health Protection Agency kindly commented on draft manuscripts. Eileen Harris and Rodney Bray at Natural History Museum are thanked for advice on parasites. Those parts of this study performed at AHVLA were funded under the Diseases of Wildlife Scheme and those performed at the Moredun Research Institute were funded by the Scottish Government Rural and Environment Science and Analytical Services Division. J. Benavides is supported by a “Ramón y Cajal” contract of the Spanish Ministry of Economy and Competitiveness. None of the authors received funding from other outside sources for this work.Peer Reviewe

A log analysis study of 10 years of ebook consumption in academic library collections

Even though libraries have been offering eBooks for more than a decade, very little is known about eBook access and consumption in academic library collections. This paper addresses this gap with a log analysis study of eBook access at the library of the University of Waikato. This in-depth analysis covers a period spanning 10 years of eBook use at this university. We draw conclusions about the use of eBooks at this institution and compare the results with other published studies of eBook usage at tertiary institutes

Interferon gamma responses to proteome-determined specific recombinant proteins: Potential as diagnostic markers for ovine Johne’s disease

Johne’s disease (JD), or paratuberculosis is a fatal enteritis of animals caused by infection with Mycobacterium avium subspecies paratuberculosis (Map). There may be a long subclinical phase with no signs of clinical disease. Diagnosis of JD is problematic and no test can reliably detect sub-clinical disease. Th1 responses to Map are believed to be activated first with a later switch to Th2 responses and progression to clinical disease. Detection of a cell-mediated response, indicated by interferon gamma (IFN-) produced in response to mycobacterial antigens, may give an early indication of infection. Crude extracts of Map (PPDj) have been used to detect the cell-mediated response, but more specific, quantifiable antigens would improve the test. Thirty Map-specific proteins were screened for their ability to raise a cell-mediated response in subclinically infected sheep. Four proteins were selected and tested using blood from subclinical animals and controls from a JD-free flock. Three proteins elicited IFN- levels which were higher in the subclinical group than in the control group, two were statistically significant. Thus these proteins have the ability to discriminate groups of infected and uninfected animals and may have use in diagnosis of JD

The combined effects of water and nitrogen on the relationship between a native hemiparasite and its invasive host.

Stem hemiparasites are dependent on their hosts for water and nitrogen. Most studies, however, assess the influence of one factor on parasite:host associations, thus limiting our mechanistic understanding of their performance in nature. We investigated the combined effects of water and nitrogen (N) availability on both host (Ulex europaeus) and parasite (Cassytha pubescens). Parasite infection significantly decreased host shoot biomass and shoot:root ratio more severely in high water than low water, irrespective of N supply. Parasite stem [N] was significantly higher in high water than low water treatments, regardless of N supply, but parasite biomass didn't vary among treatments. Irrespective of water and N supply, infected plants had significantly lower total, root and nodule biomass, predawn and midday quantum yields, maximum electron transport rates, water potentials and nitrogen concentration [N]. Parasite δ13 C was significantly higher than that of the host. Our results suggest that stem hemiparasites can better extract resources from hosts when water availability is high, resulting in greater impact on the host in these conditions. Where hemiparasitic plants are being investigated as biocontrol for invasive weeds, they may be more effective in wetter habitats than in dry ones

Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.

BACKGROUND: Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne's disease in livestock. Determining genetic diversity is prerequisite to understanding the epidemiology and biology of Map. We performed the first whole genome sequencing (WGS) of 141 global Map isolates that encompass the main molecular strain types currently reported. We investigated the phylogeny of the Map strains, the diversity of the genome and the limitations of commonly used genotyping methods. RESULTS: Single nucleotide polymorphism (SNP) and phylogenetic analyses confirmed two major lineages concordant with the former Type S and Type C designations. The Type I and Type III strain groups are subtypes of Type S, and Type B strains are a subtype of Type C and not restricted to Bison species. We found that the genome-wide SNPs detected provided greater resolution between isolates than currently employed genotyping methods. Furthermore, the SNP used for IS1311 typing is not informative, as it is likely to have occurred after Type S and C strains diverged and does not assign all strains to the correct lineage. Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) differentiates Type S from Type C but provides limited resolution between isolates within these lineages and the polymorphisms detected do not necessarily accurately reflect the phylogenetic relationships between strains. WGS of passaged strains and coalescent analysis of the collection revealed a very high level of genetic stability, with the substitution rate estimated to be less than 0.5 SNPs per genome per year. CONCLUSIONS: This study clarifies the phylogenetic relationships between the previously described Map strain groups, and highlights the limitations of current genotyping techniques. Map isolates exhibit restricted genetic diversity and a substitution rate consistent with a monomorphic pathogen. WGS provides the ultimate level of resolution for differentiation between strains. However, WGS alone will not be sufficient for tracing and tracking Map infections, yet importantly it can provide a phylogenetic context for affirming epidemiological connections

Control of bacterial nitrate assimilation by stabilization of G-quadruplex DNA

Here we present a chemical-biology study in the model soil bacterium Paracoccus denitrificans, where we show ligand-specific control of nitrate assimilation. Stabilization of a G-quadruplex in the promoter region of the nas genes, encoding the assimilatory nitrate/nitrite reductase system, is achieved using known quadruplex ligands and results in attenuation of gene transcription