Randomly primed,strand-switching,MinION-based sequencing for the detection and characterization of cultured RNA viruses     

Kelsey T. Young  Kevin K. Lahmers  Holly S. Sellers  David E. Stallknecht  Rebecca L. Poulson  Jerry T. Saliki  Stephen Mark Tompkins  Ian Padykula  Chris Siepker  Elizabeth W. Howerth  Michelle Todd  James B. Stanton 《Journal of veterinary diagnostic investigation》2021,33(2):202

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.  相似文献   

Carbon Accounting and Savanna Fire Management     

Graham von Maltitz 《African Journal of Range and Forage Science》2016,33(3):215-216

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The New Game Rancher     

Ian McDonald 《African Journal of Range and Forage Science》2016,33(4):280-281

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Australia's emergency animal disease preparedness plan     

Denney I 《Australian veterinary journal》2007,85(3):N4

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Evaluation of radiometric faecal culture and direct PCR on pooled faeces for detection of Mycobacterium avium subsp. paratuberculosis in cattle     

Eamens GJ  Whittington RJ  Turner MJ  Austin SL  Fell SA  Marsh IB 《Veterinary microbiology》2007,125(1-2):22-35

Dilution rates for pooled faecal culture (PFC) and direct IS900 polymerase chain reaction (D-PCR) tests were evaluated on faecal samples from infected cows mixed with uninfected faeces in dilutions from 1 in 5 to 1 in 50. PFC was performed by radiometric culture, with confirmation by IS900 PCR and restriction endonuclease analysis (PCR/REA) on growth, and by mycobactin dependency testing on solid medium. Using 37 culture positive faecal samples from 12 subclinical cows, 83.8% and 94.6% of samples were confirmed positive in the PFC assay at dilutions of 1 in 50 and 1 in 30, respectively. Lower dilutions (1 in 5 to 1 in 20) provided only marginally better sensitivity, and confirmation of PFC growth by PCR/REA was significantly more sensitive than mycobactin dependency. D-PCR had significantly lower sensitivity than PFC confirmed by PCR/REA, with pools of 1 in 50, 30, 10 and 5 yielding positive results in 64.9%, 70.3%, 78.4% and 83.8% of samples, respectively. Cattle considered to be shedding 1.5 x 10(6) viable M. avium subsp. paratuberculosis (Map)/g faeces (on the basis of estimated losses in processing and growth rates in radiometric broth) were positive at dilutions up to 1 in 50 in the PFC and D-PCR. Those shedding 5 x 10(5) viable Map/g were positive in the PFC at dilutions up to 1 in 40, but required a 1 in 10 dilution or less for D-PCR. The results suggest that for cattle shedding relatively high concentrations of Map in faeces (>2 x 10(5) viable Map/g), maximal dilutions of 1 in 30 for PFC and 1 in 10 for D-PCR would be applicable.  相似文献   

Incidence and effects of West Nile virus infection in vaccinated and unvaccinated horses in California     

Gardner IA  Wong SJ  Ferraro GL  Balasuriya UB  Hullinger PJ  Wilson WD  Shi PY  MacLachlan NJ 《Veterinary research》2007,38(1):109-116

A prospective cohort study was used to estimate the incidence of West Nile virus (WNV) infection in a group of unvaccinated horses (n = 37) in California and compare the effects of natural WNV infection in these unvaccinated horses to a group of co-mingled vaccinated horses (n = 155). Horses initially were vaccinated with either inactivated whole virus (n = 87) or canarypox recombinant (n = 68) WNV vaccines during 2003 or 2004, prior to emergence of WNV in the region. Unvaccinated horses were serologically tested for antibodies to WNV by microsphere immunoassay incorporating recombinant WNV E protein (rE MIA) in December 2003, December 2004, and every two months thereafter until November 2005. Clinical neurologic disease attributable to WNV infection (West Nile disease (WND)) developed in 2 (5.4%) of 37 unvaccinated horses and in 0 of 155 vaccinated horses. One affected horse died. Twenty one (67.7%) of 31 unvaccinated horses that were seronegative to WNV in December, 2004 seroconverted to WNV before the end of the study in November, 2005. Findings from the study indicate that currently-available commercial vaccines are effective in preventing WND and their use is financially justified because clinical disease only occurred in unvaccinated horses and the mean cost of each clinical case of WND was approximately 45 times the cost of a 2-dose WNV vaccination program.  相似文献   

Intra- and interobserver assessments of intestinal wall thickness and segmentations from transverse sections of feline abdominal ultrasound images     

Jasmine Chang  Ian R. Porter  Marnin A. Forman  Natalya Shcherban  Parminder S. Basran 《Veterinary radiology & ultrasound》2023,64(1):131-139

Measurements of intestinal wall thicknesses from ultrasound imaging (US) are routinely used to support diagnoses of intestinal disorders in cats, however published studies describing observer agreement are currently lacking. The aim of this retrospective, observer agreement study was to quantify inter- and intraobserver repeatability and agreement in the measurement of intestinal wall layer thicknesses and the segmentation of transverse sections of small intestines in US images of 20 cats. Intestinal wall layer thickness measurements of the mucosa, submucosa, muscularis, serosa layer, and total thickness of these layers were performed on five cats with small cell epitheliotropic lymphoma, five with inflammatory bowel disease, and 10 with other conditions. Thickness measurements and the segmentation encompassing the serosa layer were obtained from five observers four times non-sequentially. The average standard deviation in thickness measurements (95% confidence interval) in the mucosa, submucosa, muscularis, serosa, and total thickness were 0.35 (0.07–0.95), 0.24 (0.07-0.52), 0.22 (0.06-0.49), 0.20 (0.05-0.49), and 0.57 (0.11-1.60) mm, respectively. The average intraclass correlation coefficients, which estimates the degree of consistency in thickness measurements and segmentation areas for each observer, ranged from 0.355 to 0.870 and 0.850 to 0.993, respectively. The interclass correlation coefficient, which estimates the degree of consistency when measuring a thickness or segmentation area over all observers ranged from 0.115 to 0.753, and 0.811 to 0.902, respectively. The overall average Dice Coefficient, which estimates the extent of overlap of the segmentations for all observers was 0.957 (0.933 to 0.972). Our results suggest segmentations of small intestines have a higher interobserver agreement than measurements of intestinal wall thicknesses.  相似文献   

Thoracolumbar myelopathies in pug dogs     

Ian J. Wachowiak  Jon S. Patterson  Kathryn M. Winger  Kathleen L. Smiler  Robert Cole  Rachel Moon  Michael Kluz  Lisa R. Bartner 《Journal of veterinary internal medicine / American College of Veterinary Internal Medicine》2023,37(2):618-625

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Evaluation of a novel moving threshold gating strategy for assessment of reticulated platelets in dogs using the ADVIA 2120 analyzer     

Anja Kuhn  Kristina Weiler  Graham Gibbs  Gottfried Prechtl  Natali Bauer  Andreas Moritz 《Veterinary clinical pathology / American Society for Veterinary Clinical Pathology》2023,52(1):11-21

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The River Wadu role play — ten years experience     

Ian Carruthers  Laurence Smith 《Irrigation and Drainage Systems》1989,3(3):281-308

This paper describes a role playing planning exercise that has been used for training agriculturists, engineers and agricultural economists for more than ten years. It sets out the objectives and key features of the exercise and the experience that has been gained in its use. The exercise has been found to successfully test and integrate subject matter expertise acquired from formal teaching. It also highlights the multiple and often conflicting objectives of irrigation planning, and the need for full evaluation of alternatives and sound technical judgements under conditions of inadequate data and time pressure. The exercise is also successful in developing professional personal skills such as group working, interviewing and presentation, and is recommended as an effective training aid.  相似文献