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

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.     

Socio-spatial organization reveals paternity and low kinship in the Honduran white bat (Ectophylla alba) in Costa Rica

Ectophylla alba is a tent-making bat that roosts in mixed-sex clusters comprising adults and offspring. Our goal was to determine the genetic identity of individuals belonging to different roosting groups. We tested the hypothesis of kin selection as a major force structuring group composition. We used 9 microsatellites designed for E. alba to determine the genetic identity and probability of parentage of individuals. We analyzed parentage and kinship using the software ML-Relate, GenAIEx, and Cervus. The obtained relationship probabilities (0.5) revealed a clear maternal relationship between female adults and offspring with allele compatibility, and at least 5 relationships between male adults and pups. We found a low degree of relatedness within roosting groups. Between roosting groups at different sites, the mean probability of a half-sibling relationship ranged from 0.214 to 0.244 and, for full-sibling relationship, from 0.383 to 0.553. Genetically, adult individuals were poorly related within clusters, and kinship as an evolutionary force could not explain group membership.     

Effects of Annealing and Concentration of Calcium Salts on Thermal and Rheological Properties of Maize Starch During an Ecological Nixtamalization Process

The objective of the present work was to study the effect of annealing and concentration of Ca(OH)₂ (lime) and calcium salts on the thermal and rheological properties of maize starch during an ecological nixtamalization process. Thermal and rheological properties of maize starch changed during the ecological nixtamalization process because of three main causes: the annealing phenomenon, type of calcium salt, and calcium salt concentration. In all treatments thermal properties (T_o, T_p, and T_f) of nixtamal starch increased owing to the annealing process, whereas the type of salt or lime increased thermal properties and decreased pasting properties in this order: CaCl₂ > CaSO₄ > Ca(OH)₂ ≈ CaCO₃. This behavior was because of the dissociation of each salt or lime in water. Anions (OH⁻) can penetrate much more easily into the starch granule and start the gelatinization process by rupturing hydrogen bonds. Additionally, amylose‐lipid complexes were formed during the nixtamalization processes, as indicated by an increasing peak at 4.5 Å in X‐ray diffraction patterns.     

IMAGING DIAGNOSIS—MULTIMODALITY FINDINGS IN AN ADULT DOG WITH PRIMARY SARCOMA OF THE PULMONARY ARTERY AND MYOCARDIAL METASTASES

Intravascular pulmonary artery sarcomas in combination with myocardial metastasis are rare in dogs. We describe the radiographic, echocardiographic, and electrocardiographic‐gated (ECG‐gated) computed tomographic angiography (CTA) findings in a dog with pulmonary artery sarcoma. All imaging studies demonstrated severe main pulmonary artery enlargement. Echocardiography and ECG‐gated CTA revealed a mass occluding the lumen of the right pulmonary artery. In addition, CTA revealed focal left ventricular myocardial contrast enhancement and parenchymal lung changes. Postmortem examination confirmed the presence of a large thrombus associated with arteriosclerosis and an intravascular sarcoma in the right pulmonary artery with metastases to the myocardium, lungs and brain.     

INVITED REVIEW—IMAGE REGISTRATION IN VETERINARY RADIATION ONCOLOGY: INDICATIONS,IMPLICATIONS, AND FUTURE ADVANCES

The field of veterinary radiation therapy (RT) has gained substantial momentum in recent decades with significant advances in conformal treatment planning, image‐guided radiation therapy (IGRT), and intensity‐modulated (IMRT) techniques. At the root of these advancements lie improvements in tumor imaging, image alignment (registration), target volume delineation, and identification of critical structures. Image registration has been widely used to combine information from multimodality images such as computerized tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) to improve the accuracy of radiation delivery and reliably identify tumor‐bearing areas. Many different techniques have been applied in image registration. This review provides an overview of medical image registration in RT and its applications in veterinary oncology. A summary of the most commonly used approaches in human and veterinary medicine is presented along with their current use in IGRT and adaptive radiation therapy (ART). It is important to realize that registration does not guarantee that target volumes, such as the gross tumor volume (GTV), are correctly identified on the image being registered, as limitations unique to registration algorithms exist. Research involving novel registration frameworks for automatic segmentation of tumor volumes is ongoing and comparative oncology programs offer a unique opportunity to test the efficacy of proposed algorithms.     

A SURVEY OF RADIOLOGISTS AND REFERRING VETERINARIANS REGARDING IMAGING REPORTS

An imaging report is a vital communication tool between a radiologist and clinician. In a field where in‐person communication may not be readily available, it is imperative that the report clearly relays pertinent clinical information in a timely manner. The purpose of this observational study was to describe and compare opinions and expectations of small animal general practitioners, veterinary specialists, and veterinary radiologists regarding the imaging report. Online surveys were distributed, and data were collected from 202 veterinary clinicians and 123 veterinary radiologists. The majority (89%) of clinicians were satisfied with their imaging reports and stated that they read the radiology report as soon as it was available (92%). Just less than half (48%) of clinicians indicated it was standard of care that a board‐certified veterinary radiologist read all imaging studies. Radiologists and clinicians agreed that a clinical history (98% and 94%, respectively) and clinical question (82% and 68%, respectively) were needed to generate a good radiology report. Fifty‐five percent to 70% of clinicians prefer red bulleted reports, which included incidental findings (96%); while radiologists slightly favored prose reporting (37–46%). Clinicians found it helpful when additional imaging (86%), medical (71%), and surgical recommendations (73%) were made. About one‐third of specialists who had been in practice for >11 years thought they were better able to interpret imaging for their own specialty than the radiologist. Clinicians voiced discontentment with reports that were not completed in a timely manner or did not give a prioritized differential list. Further studies are warranted to provide a more in‐depth evaluation of veterinary radiology reporting structure and style.     

Characterization and application of lactic acid bacteria for tropical silage preparation

Strains TH 14, TH 21 and TH 64 were isolated from tropical silages, namely corn stover, sugar cane top and rice straw, respectively, prepared in Thailand. These strains were selected by low pH growth range and high lactic acid‐producing ability, similar to some commercial inoculants. Based on the analysis of 16S ribosomal RNA gene sequence and DNA‐DNA relatedness, strain TH 14 was identified as Lactobacillus casei, and strains TH 21 and TH 64 were identified as L. plantarum. Strains TH 14, TH 21, TH 64 and two commercial inoculants, CH (L. plantarum) and SN (L. rhamnosus), were used as additives to fresh and wilted purple Guinea and sorghum silages prepared using a small‐scale fermentation method. The number of epiphytic lactic acid bacteria (LAB) in the forages before ensilage was relatively low but the numbers of coliform and aerobic bacteria were higher. Sorghum silages at 30 days of fermentation were all well preserved with low pH (3.56) and high lactic acid production (72.86 g/kg dry matter). Purple Guinea silage inoculated with LAB exhibited reduced count levels of aerobic and coliform bacteria, lower pH, butyric acid and ammonia nitrogen and increased lactic acid concentration, compared with the control. Strain TH 14 more effectively improved lactic acid production compared with inoculants and other strains. © 2016 Japanese Society of Animal Science