Viral Diversity in Mixed Tree Fruit Production Systems Determined through Bee-Mediated Pollen Collection.

Commercially cultivated species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (), another member of the and distantly related to , can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites.

Plant virus diversity in bee and pollen samples from apple () and sweet cherry () agroecosystems.

Introduction: Honey bee () pollination is widely used in tree fruit production systems to improve fruit set and yield. Many plant viruses can be associated with pollen or transmitted through pollination, and can be detected through bee pollination activities. Honey bees visit multiple plants and flowers in one foraging trip, essentially sampling small amounts of pollen from a wide area.

Survey of Diversity Reveals as a Potential Phytophthora Root Rot Pathogen in Québec Christmas Tree Plantations.

Christmas trees are an economically and culturally important ornamental plant in North America. Many microorganisms are pathogens of firs cultivated as Christmas trees. Among those, causes millions of dollars in damage to plantations annually.

Ultrafast laser writing of arbitrary long low-loss waveguides in optical fibers.

We propose an innovative femtosecond laser writing approach, based on a reel-to-reel configuration, allowing the fabrication of arbitrary long optical waveguides in coreless optical fibers directly through the coating. We report few meters long waveguides operating in the near-infrared (near-IR) with propagation losses as low as 0.055 ± 0.

Biomonitoring of Fungal and Oomycete Plant Pathogens by Using Metabarcoding.

Fungal and oomycete plant pathogens are responsible for the devastation of various ecosystems such as forest and crop species worldwide. In an effort to protect such natural resources for food, lumber, etc., early detection of non-indigenous phytopathogenic fungi in new areas is a key approach in managing threats at their source of introduction.

Four In Silico Designed and Validated qPCR Assays to Detect and Discriminate and , Individually or as a Complex.

Several fungi classified in the genus are well-known to infect grass species including wheat (). is a highly unwanted wheat pathogen causing Karnal bunt, subject to quarantine regulations in many countries. Historically, suspected Karnal bunt infections were identified by morphology, a labour-intensive process to rule out other tuberculate-spored species that may be found as contaminants in grain shipments, and the closely-related pathogen on ryegrass ().

Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada.

Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous.

A Wireless Electro-Optic Platform for Multimodal Electrophysiology and Optogenetics in Freely Moving Rodents.

This paper presents the design and the utilization of a wireless electro-optic platform to perform simultaneous multimodal electrophysiological recordings and optogenetic stimulation in freely moving rodents. The developed system can capture neural action potentials (AP), local field potentials (LFP) and electromyography (EMG) signals with up to 32 channels in parallel while providing four optical stimulation channels. The platform is using commercial off-the-shelf components (COTS) and a low-power digital field-programmable gate array (FPGA), to perform digital signal processing to digitally separate in real time the AP, LFP and EMG while performing signal detection and compression for mitigating wireless bandwidth and power consumption limitations.

100-W-level single-mode ytterbium-free erbium fiber laser.

We report on an ytterbium-free, erbium-doped single-mode all-fiber laser reaching a record output power of 107 W at 1598 nm, with a slope efficiency of 38.6% according to the absorbed pump power at 981 nm. The erbium-doped gain fiber, co-doped with cerium, aluminum, and phosphorus, was fabricated in-house with adjusted doping concentrations to reduce erbium ions clustering, thereby increasing efficiency while keeping the numerical aperture low to ensure a single-mode laser operation.

In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols.

This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification.

Curvature sensing using a hybrid polycarbonate-silica multicore fiber.

We report on the development of a novel hybrid glass-polymer multicore fiber integrating three 80 µm polyimide-coated silica fibers inside a 750 µm polycarbonate cladding. By inscribing an array of distributed FBGs along each segment of silica fiber prior to the hybrid fiber drawing, we demonstrate a curvature sensor with an unprecedented precision of 296 pm/m around 1550 nm, about 7 times more sensitive than sensors based on standard 125 µm multicore fibers. As predicted by theory, we show experimentally that the measured curvature is insensitive to temperature and strain.

Author Correction: Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Monitoring of Primary and Secondary Inoculum by Real-Time qPCR.

Onion downy mildew (ODM), caused by , is a serious threat for onion growers worldwide. In southwestern Québec, Canada, a steady increase in occurrence of ODM has been observed since the mid-2000s. On onion, can develop local and systemic infections producing numerous sporangia which act as initial inoculum locally and also for neighboring areas.

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists.

High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools.

Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov.

Apple bitter rot caused by Colletotrichum species is a growing problem worldwide. Colletotrichum spp. are economically important but taxonomically un-resolved.

Validation of a Preformulated, Field Deployable, Recombinase Polymerase Amplification Assay for Species.

Recombinase polymerase amplification (RPA) assays are valuable molecular diagnostic tools that can detect and identify plant pathogens in the field without time-consuming DNA extractions. Historically, RPA assay reagents were commercially available as a lyophilized pellet in microfuge strip tubes, but have become available in liquid form more recently-both require the addition of primers and probes prior to use, which can be challenging to handle in a field setting. Lyophilization of primers and probes, along with RPA reagents, contained within a single tube limits the risk of contamination, eliminates the need for refrigeration, as the lyophilized reagents are stable at ambient temperatures, and simplifies field use of the assays.

In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR.

Global trade and climate change are responsible for a surge in foreign invasive species and emerging pests and pathogens across the world. Early detection and surveillance activities are essential to monitor the environment and prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process.

Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols.

This paper presents the performance of two eukaryotic genomic ribosomal regions, ITS1 and ITS2, in describing fungal diversity in aerosol samples using amplicon-based High-Throughput Sequencing (HTS). Composting sites, biomethanization facilities, and dairy farms, all affected by the presence of fungi, were visited to collect air samples. The amplicon-based HTS approach is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing.

The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.