Diagnostics of viral infections using high-throughput genome sequencing data.

Plant viral infections cause significant economic losses, totalling $350 billion USD in 2021. With no treatment for virus-infected plants, accurate and efficient diagnosis is crucial to preventing and controlling these diseases. High-throughput sequencing (HTS) enables cost-efficient identification of known and unknown viruses.

Real-time attending trauma surgeon assessment of direct-to-operating room trauma resuscitations: Results from a prospective observational study.

Background: Direct-to-operating room (DOR) resuscitation expedites interventions for trauma patients. Perceived benefit from the surgeon's perspective is not well known. This study assesses the integration of a real-time surgeon assessment tool into a DOR protocol.

Improving grapevine virus diagnostics: Comparative analysis of three dsRNA enrichment methods for high-throughput sequencing.

The extraction of double stranded (ds) RNA is a common enrichment method for the study, characterization, and detection of RNA viruses. In addition to RNA viruses, viroids, and some DNA viruses, can also be detected from dsRNA enriched extracts which makes it an attractive method for detecting a wide range of viruses when coupled with HTS. Several dsRNA enrichment strategies have been developed.

Choosing wisely: A prospective study of direct to operating room trauma resuscitation including real-time trauma surgeon after-action review.

Introduction: Although several centers have direct to operating room (DOR) resuscitation programs, there are no published prospective studies on optimal patient selection, interventions, outcomes, or real-time surgeon assessments.

Methods: Direct to operating room cases for 1 year were prospectively enrolled. Demographics, injury types/severity, triage criteria, interventions, and outcomes including Glasgow Outcome Scale score were collected.

Into the wild and on to the table: A Western Trauma Association multicenter analysis and comparison of wilderness falls in rock climbers and nonclimbers.

Background: Wilderness activities expose outdoor enthusiasts to austere environments with injury potential, including falls from height. The majority of published data on falls while climbing or hiking are from emergency departments. We sought to more accurately describe the injury pattern of wilderness falls that lead to serious injury requiring trauma center evaluation and to further distinguish climbing as a unique pattern of injury.

Direct to operating room trauma resuscitation: Optimizing patient selection and time-critical outcomes when minutes count.

Background: Although several trauma centers have developed direct to operating room (DOR) trauma resuscitation programs, there is little published data on optimal patient selection, practices, and outcomes. We sought to analyze triage criteria and interventions associated with optimal DOR outcomes and resource utilization.

Methods: Retrospective review of all adult DOR resuscitations for a 6-year period was performed.

Discovery of Negative-Sense RNA Viruses in Trees Infected with Apple Rubbery Wood Disease by Next-Generation Sequencing.

Apple rubbery wood is a disease of apple found around the world, often associated with Apple flat limb disease, and regulated in many countries. Despite its long history in apple cultivation, the disease's causal agent has remained elusive. In this study, next-generation sequencing (NGS) was used to identify and characterize several related novel viral agents from apple rubbery wood-infected plants, which have been named Apple rubbery wood virus (ARWV) 1 and 2.

Comparative analysis of cherry virus A genome sequences assembled from deep sequencing data.

Cherry virus A (CVA) is a ubiquitous graft-transmissible virus that mainly infects Prunus spp. Next-generation sequencing was applied to 39 tree fruit specimens infected with CVA, and 75 full and 16 partial-length CVA genome sequences were assembled. Phylogenetic analysis of these and 11 previously sequenced CVA genomes resulted in six major clusters with no observable relationship between the host and the assembled genome sequences.

Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control.

The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics.

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

Background: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G.

Complete genome sequence of three tomato ringspot virus isolates: evidence for reassortment and recombination.

The genome sequence of tomato ringspot virus (ToRSV, a subgroup C nepovirus) is currently available for one raspberry isolate. In this study, we describe the complete genome sequence of three additional isolates from raspberry (Rasp1-2014), grapevine (GYV-2014) and prunus (13C280). The degree of nucleotide sequence identity shared between RNA1 and RNA2 in the 5'-terminal 900 nucleotides and 3' untranslated region varied from 98-99 % (13C280, GYV-2014) to 80 % (Rasp1-2014).

Amplification-free detection of grapevine viruses using an oligonucleotide microarray.

A single-colour microarray hybridization system was designed and evaluated for the detection of viruses infecting grapevine. Total RNA (≥0.5μg) from infected plants was converted to cDNA and labelled with Cy3 using two different strategies.

Occurrence and Detection of Globodera rostochiensis on Vancouver Island, British Columbia: An Update.

The potato cyst nematode (PCN), Globodera rostochiensis, has been present in Central Saanich on Vancouver Island for at least 45 years. Eradication/control efforts have been ongoing, with regulations enacted in the early 1980s restricting the planting of host crops and movement of soil. Surveys monitoring for cyst populations have been minimal since the regulations have been in place with only one limited study in the early 1990s.

Detection of genetically modified canola using multiplex PCR coupled with oligonucleotide microarray hybridization.

A rapid method was developed for concurrent screening of transgenic elements in GM canola. This method utilizes a single multiplex PCR coupled with an oligonucleotide DNA array capable of simultaneously detecting the 12 approved GM canola lines in Canada. The assay includes construct-specific elements for identification of approved lines, common elements (e.

Real-time polymerase chain reaction (PCR) quantitative detection of Brassica napus using a locked nucleic acid TaqMan probe.

Several countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms. Real-time quantitative Polymerase Chain Reaction (PCR) has quickly become the method of choice in support of these regulations and requires the development of separate PCR assays targeting the transgenic sequence as well as a specific endogenous gene sequence. To develop a Brassica napus-specific PCR assay, partial sequences of the acetyl-CoA carboxylase BnACCg8 gene from B.

Detection and quantification of roundup ready soy in foods by conventional and real-time polymerase chain reaction.

Transgenic soybean line GTS-40-3-2, marketed under the trade name Roundup Ready (RR) soy, was developed by Monsanto (USA) to allow for the use of glyphosate, the active ingredient of the herbicide Roundup, as a weed control agent. RR soy was first approved in Canada for environmental release and for feed products in 1995 and later for food products in 1996 and is widely grown in Canada. Consumer concern issues have resulted in proposed labeling regulations in Canada for foods derived from genetically engineered crops.