Michael G. Becker
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View article: Gene expression landscape of the <i>Brassica napus</i> seed reveals subgenome bias in both space and time
Gene expression landscape of the <i>Brassica napus</i> seed reveals subgenome bias in both space and time Open
Brassica napus (canola; AnAnCnCn) contains both complete diploid genomes from its progenitors Brassica rapa (An) and Brassica oleracea (Cn). Despite growing knowledge of the gene expression landscape of the B. napus seed, little is known a…
View article: Identification of circulating human papillomavirus types through high-throughput sequencing of Canadian municipal and institutional wastewater samples
Identification of circulating human papillomavirus types through high-throughput sequencing of Canadian municipal and institutional wastewater samples Open
Human papillomaviruses (HPVs) are a diverse group of viruses that infect human mucosal and cutaneous tissues, with a ubiquitous global distribution. Several types are classified as high-risk due to their association with cervical, anal, pe…
View article: Post-market surveillance of six COVID-19 point-of-care tests using pre-Omicron and Omicron SARS-CoV-2 variants
Post-market surveillance of six COVID-19 point-of-care tests using pre-Omicron and Omicron SARS-CoV-2 variants Open
Post-market surveillance of test performance is a critical function of public health agencies and clinical researchers that ensures tests maintaining diagnostic characteristics following their regulatory approval. Changes in product qualit…
View article: Post-Market Surveillance of Six COVID-19 Point-of-Care Tests Using Pre-Omicron and Omicron SARS-CoV-2 Variants
Post-Market Surveillance of Six COVID-19 Point-of-Care Tests Using Pre-Omicron and Omicron SARS-CoV-2 Variants Open
Post-market surveillance of test performance is a critical function of public health agencies and clinical researchers that ensures diagnostics maintain performance characteristics following their regulatory approval. Changes in product qu…
View article: Changing patterns of otitis media in the Waikato region during the COVID-19 pandemic
Changing patterns of otitis media in the Waikato region during the COVID-19 pandemic Open
Introduction Acute otitis media (AOM) is a common condition of children encountered in general practice. A proportion of children develop otitis media with effusion (OME), which may require tympanostomy and ventilation tube insertion. Aim …
View article: Clinical evaluation of the GeneXpert <sup>®</sup> Xpert <sup>®</sup> Xpress SARS-CoV-2/Flu/RSV PLUS combination test
Clinical evaluation of the GeneXpert <sup>®</sup> Xpert <sup>®</sup> Xpress SARS-CoV-2/Flu/RSV PLUS combination test Open
The GeneXpert ® Xpert ® Xpress SARS-CoV-2/Flu/RSV PLUS combination test (PLUS assay) received Health Canada approval in January 2022. The PLUS assay is similar to the SARS-CoV-2/Flu/RSV combination test, with modifications to improve assay…
View article: Clinical Evaluation of the GeneXpert<sup>®</sup>Xpert<sup>®</sup>Xpress SARS-CoV-2/Flu/RSV<i>PLUS</i>Combination Test
Clinical Evaluation of the GeneXpert<sup>®</sup>Xpert<sup>®</sup>Xpress SARS-CoV-2/Flu/RSV<i>PLUS</i>Combination Test Open
The GeneXpert ® Xpert ® Xpress SARS-CoV-2/Flu/RSV PLUS combination test ( PLUS Assay) received Health Canada approval in January 2022. The PLUS Assay is similar to the SARS-CoV-2/Flu/RSV combination test, with modifications to improve assa…
View article: Generation of False-Positive SARS-CoV-2 Antigen Results with Testing Conditions outside Manufacturer Recommendations: A Scientific Approach to Pandemic Misinformation
Generation of False-Positive SARS-CoV-2 Antigen Results with Testing Conditions outside Manufacturer Recommendations: A Scientific Approach to Pandemic Misinformation Open
With the Panbio severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen test being deployed in over 120 countries worldwide, understanding conditions required for its ideal performance is critical. Recently on social media, th…
View article: A sensitive and rapid wastewater test for SARS-COV-2 and its use for the early detection of a cluster of cases in a remote community
A sensitive and rapid wastewater test for SARS-COV-2 and its use for the early detection of a cluster of cases in a remote community Open
Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the nee…
View article: Generation of false positive SARS-CoV-2 antigen results with testing conditions outside manufacturer recommendations: A scientific approach to pandemic misinformation
Generation of false positive SARS-CoV-2 antigen results with testing conditions outside manufacturer recommendations: A scientific approach to pandemic misinformation Open
Objectives Antigen-based rapid diagnostics tests (Ag-RDTs) are useful tools for SARS-CoV-2 detection. However, misleading demonstrations of the Abbott Panbio COVID-19 Ag-RDT on social media claimed that SARS-CoV-2 antigen could be detected…
View article: Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay
Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay Open
The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. In po…
View article: Global RNA sequencing reveals enhanced photosynthetic activity and auxin response in<i>Brassica napus</i>treated with<i>Pseudomonas chlororaphis</i>PA23
Global RNA sequencing reveals enhanced photosynthetic activity and auxin response in<i>Brassica napus</i>treated with<i>Pseudomonas chlororaphis</i>PA23 Open
Plant growth promoting bacteria (PGPB) are a growing subset of agricultural adjuncts which can be used to increase crop yield and plant productivity. Although substantial research has been conducted on the metabolites and active molecules …
View article: Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays
Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays Open
Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays outperform conventional Sanger sequencing in scalability, sensitivity, and quantitative detection of minority resistance variants. Thus far, HIVDR assays have been a…
View article: Recommendations for sample pooling on the Cepheid GeneXpert<sup>®</sup>system using the Cepheid Xpert<sup>®</sup>Xpress SARS-CoV-2 assay
Recommendations for sample pooling on the Cepheid GeneXpert<sup>®</sup>system using the Cepheid Xpert<sup>®</sup>Xpress SARS-CoV-2 assay Open
The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. Here,…
View article: Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23
Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23 Open
Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several inhibitory compounds that are under control of a co…
View article: Investigation of the quorum-sensing regulon of the biocontrol bacterium <i>Pseudomonas chlororaphis</i> strain PA23
Investigation of the quorum-sensing regulon of the biocontrol bacterium <i>Pseudomonas chlororaphis</i> strain PA23 Open
Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum . PA23 produces several of inhibitory compounds that are under control of …
View article: Transcriptome landscape of the early <i>Brassica napus</i> seed
Transcriptome landscape of the early <i>Brassica napus</i> seed Open
Brassica napus L. (canola) is one of the world's most economically important oilseeds. Despite our growing knowledge of Brassica genetics, we still know little about the genes and gene regulatory networks underlying early seed development.…
View article: Transcriptome Analysis of <i>Rlm2</i>-Mediated Host Immunity in the <i>Brassica napus</i>–<i>Leptosphaeria maculans</i> Pathosystem
Transcriptome Analysis of <i>Rlm2</i>-Mediated Host Immunity in the <i>Brassica napus</i>–<i>Leptosphaeria maculans</i> Pathosystem Open
Our study investigated disease resistance in the Brassica napus–Leptosphaeria maculans pathosystem using a combination of laser microdissection, dual RNA sequencing, and physiological validations of large-scale gene sets. The use of laser …
View article: RNA sequencing of Brassica napus reveals cellular redox control of Sclerotinia infection
RNA sequencing of Brassica napus reveals cellular redox control of Sclerotinia infection Open
Brassica napus is one of the world's most valuable oilseeds and is under constant pressure by the necrotrophic fungal pathogen, Sclerotinia sclerotiorum, the causal agent of white stem rot. Despite our growing understanding of host pathoge…
View article: The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks
The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks Open
In addition to directly antagonizing S. sclerotiorum, PA23 primes the plant defense response through induction of unique local and systemic defense networks. This study provides novel insight into the effects of biocontrol agents applied t…
View article: SeqEnrich: A tool to predict transcription factor networks from co-expressed Arabidopsis and Brassica napus gene sets
SeqEnrich: A tool to predict transcription factor networks from co-expressed Arabidopsis and Brassica napus gene sets Open
Transcription factors and their associated DNA binding sites are key regulatory elements of cellular differentiation, development, and environmental response. New tools that predict transcriptional regulation of biological processes are va…
View article: Transcriptome analysis of the <i>Brassica napus</i>–<i>Leptosphaeria maculans</i> pathosystem identifies receptor, signaling and structural genes underlying plant resistance
Transcriptome analysis of the <i>Brassica napus</i>–<i>Leptosphaeria maculans</i> pathosystem identifies receptor, signaling and structural genes underlying plant resistance Open
Summary The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant loss of yield worldwide. While genetic resistance has been used to mi…
View article: Additional file 6: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks
Additional file 6: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks Open
Dataset S3. GO terms enriched in shared and uniquely-expressed genes between treatment groups, with associated log10 p-values for each treatment. List of GO terms was generated via analysis of lists of genes grouped from Fig. 2a in CanEnri…
View article: Additional file 4: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks
Additional file 4: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks Open
Dataset S2. ncbi-BLAST results of unmapped transcripts assembled with Trinity to Brassicaceae nucleotide database. (XLSX 3895Â kb)
View article: Additional file 8: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks
Additional file 8: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks Open
Dataset S4. List of genes comprising each dominant pattern (DP) of expression seen in Additional file 2: Figure S2. (XLSX 291Â kb)
View article: Additional file 9: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks
Additional file 9: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks Open
Dataset S5. Gene names, log2 fold change values and corresponding gene ontology (GO) term for select chloroplast-related GO terms. (XLSX 29Â kb)
View article: Additional file 3: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks
Additional file 3: of The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks Open
Dataset S1. Trinity transcriptome assembly of unmapped reads from control treatment groups. (FASTA 51567Â kb)
View article: Tissue-specific laser microdissection of the<i>Brassica napus</i>funiculus improves gene discovery and spatial identification of biological processes
Tissue-specific laser microdissection of the<i>Brassica napus</i>funiculus improves gene discovery and spatial identification of biological processes Open
The three primary tissue systems of the funiculus each undergo unique developmental programs to support the growth and development of the filial seed. To understand the underlying transcriptional mechanisms that orchestrate development of …