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Abstract Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call “Whole Exome Genome Sequencing” (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed). We experimentally assess the performance of WEGS with four different depth of coverage and sample multiplexing configurations. We show that the optimal WEGS configurations are 1.7–2.0 times cheaper than standard WES (no-plexing), 1.8–2.1 times cheaper than high-depth WGS, reach similar recall and precision rates in detecting coding variants as WES, and capture more population-specific variants in the rest of the genome that are difficult to recover when using genotype imputation methods. We apply WEGS to 862 patients with peripheral artery disease and show that it directly assesses more known disease-associated variants than a typical genotyping array and thousands of non-imputable variants per disease-associated locus.

Abstract Background Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province. Methods Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus. Results Conservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and “snowbird” destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7–12 led to the largest transmission lineages of the first wave (accounting for 52–75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Conclusions Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.

Abstract Background For dogs and cats, chemoprophylaxis with macrocyclic lactone (ML) preventives for heartworm disease is widely used in the United States and other countries. Since 2005, cases of loss of efficacy (LOE) of heartworm preventives have been reported in the U.S. More recently, ML-resistant D. immitis isolates were confirmed. Previous work identified 42 genetic markers that could predict ML response in individual samples. For field surveillance, it would be more appropriate to work on microfilarial pools from individual dogs with a smaller subset of genetic markers. Methods MiSeq technology was used to identify allele frequencies with the 42 genetic markers previously reported. Microfilaria from ten well-characterized new isolates called ZoeKY, ZoeMI, ZoeGCFL, ZoeAL, ZoeMP3, ZoeMO, ZoeAMAL, ZoeLA, ZoeJYD-34, and Metairie were extracted from fresh blood from dogs. DNA were extracted and sequenced with MiSeq technology. Allele frequencies were calculated and compared with the previously reported susceptible, LOE, and resistant D. immitis populations. Results The allele frequencies identified in the current resistant and susceptible isolates were in accordance with the allele frequencies previously reported in related phenotypes. The ZoeMO population, a subset of the ZoeJYD-34 population, showed a genetic profile that was consistent with some reversion towards susceptibility compared with the parental ZoeJYD-34 population. The Random Forest algorithm was used to create a predictive model using different SNPs. The model with a combination of three SNPs (NODE_42411_RC, NODE_21554_RC, and NODE_45689) appears to be suitable for future monitoring. Conclusions MiSeq technology provided a suitable methodology to work with the microfilarial samples. The list of SNPs that showed good predictability for ML resistance was narrowed. Additional phenotypically well characterized D. immitis isolates are required to finalize the best set of SNPs to be used for large scale ML resistance screening.

Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.

Peroxisome proliferator-activated receptor alpha (PPARα) is a member of the steroid hormone receptor super family involved in the control of cellular lipid utilization. This makes PPARα a candidate gene for type 2 diabetes and dyslipidemia. The aim of this study was to investigate whether genetic variation in the human PPARα gene can influence the risk of type 2 diabetes and dyslipidemia among French Canadians. We therefore first determined the genomic structure of human PPARα, and then designed intronic primers to sequence the coding region and the exon–intron boundaries of the gene in 12 patients with type 2 diabetes and in 2 nondiabetic subjects. Sequence analysis revealed the presence of a L162V missense mutation in exon 5 of one diabetic patient. Leucine 162 is contained within the DNA binding domain of the human PPARα gene, and is conserved among humans, mice, rats, and guinea pigs. We subsequently screened a sample of 121 patients newly diagnosed with type 2 diabetes and their age and sex-matched nondiabetic controls, recruited from the Saguenay-Lac-St-Jean region of Northeastern Quebec, for the presence of the L162V mutation by a PCR-RFLP based method. There was no difference in L162 homozygote or V162 carrier frequencies between diabetics and nondiabetics. However, whether diabetic or not, carriers of the V162 allele had higher plasma apolipoprotein B levels compared to noncarriers (P = =0.05). To further this association, we screened another sample of 193 nondiabetic subjects recruited in the greater Quebec City area.Carriers of the V162 allele compared with homozygotes of the L162 allele had significantly higher concentrations of plasma total and LDL-apolipoprotein B as well as LDL cholesterol (P ≤ 0.02). These results suggest an association between the PPARα V162 allele and the atherogenic/hyperapolipoprotein B dyslipidemia.

Familial clustering of colorectal cancer occurs in 15-20% of cases, however recognized cancer syndromes explain only a small fraction of this disease. Thus, the genetic basis for the majority of hereditary colorectal cancer remains unknown. EPHB2 has recently been implicated as a candidate tumor suppressor gene in colorectal cancer. The aim of this study was to evaluate the contribution of EPHB2 to hereditary colorectal cancer. We screened for germline EPHB2 sequence variants in 116 population-based familial colorectal cancer cases by DNA sequencing. We then estimated the population frequencies and characterized the biological activities of the EPHB2 variants identified. Three novel nonsynonymous missense alterations were detected. Two of these variants (A438T and G787R) result in significant residue changes, while the third leads to a conservative substitution in the carboxy-terminal SAM domain (V945I). The former two variants were found once in the 116 cases, while the V945I variant was present in 2 cases. Genotyping of additional patients with colorectal cancer and control subjects revealed that A438T and G787R represent rare EPHB2 alleles. In vitro functional studies show that the G787R substitution, located in the kinase domain, causes impaired receptor kinase activity and is therefore pathogenic, whereas the A438T variant retains its receptor function and likely represents a neutral polymorphism. Tumor tissue from the G787R variant case manifested loss of heterozygosity, with loss of the wild-type allele, supporting a tumor suppressor role for EPHB2 in rare colorectal cancer cases. Rare germline EPHB2 variants may contribute to a small fraction of hereditary colorectal cancer.

Oat (Avena sativa L.) is the main species used as a companion crop when establishing perennial forages in eastern Canada, and, although other annual species are used, they have not been systematically evaluated. A field study was conducted across five environments to contrast the use of six annual species (berseem clover, Trifolium alexandrinum L.; forage peas, Pisum sativum L.; annual ryegrass, Lolium multiflorum Lamarck; oat; Japanese millet, Echinochloa esculenta [A. Braun] H. Scholz; sudangrass, Sorghum × drummondii [Nees ex. Steud.] Millsp. & Chase) as companion crops for the establishment of alfalfa (Medicago sativa L.)‐timothy (Phleum pratense L.) mixtures. The control treatment consisted of the perennial species seeded without companion crop. Treatments were seeded at three dates and evaluated during the seeding and post‐seeding years. The performance of the six companion crops evaluated herein varied depending on the seeding date and the environment. For a mid‐May to early June seeding total seeding year forage mass was greatest with use of oat, Japanese millet, or sudangrass as companion crops; for a mid‐June to late June seeding with Japanese millet or sudangrass; and for a late July to early August seeding with oat or Japanese millet. These species, however, reduced in some environments seeding year alfalfa or timothy mass compared to a control seeded without a companion crop. Such reduction was also observed in some environments in the first post‐seeding year. Companion crop choice to establish alfalfa–timothy mixtures needs to take into consideration seeding date and forage needs on the short term versus the long term. Core Ideas: Oat is the main companion crop used to establish perennial forages, others can be used but information is limited.Use of oat, Japanese millet, or sudangrass as companion crop produce the greatest seeding year total forage mass.Most productive companion crop species resulted in 19%–31% reduction in first post‐seeding year forage mass.Use of berseem clover, annual ryegrass, and peas minimally impacted seeding and post‐seeding year forage mass.Selection of companion crops must consider seeding date and short‐ and long‐term forage needs. [ABSTRACT FROM AUTHOR]

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There is a lack of persistent forage legumes for permanent pastures in eastern Canada. Kura clover (Trifolium ambiguum M. Bieb.; KC) is a long‐lived species, with demonstrated potential in various regions, however, there is a lack of information on its performance in mixtures with grasses and no comparisons with white clover (Trifolium repens L.; WC), the main legume species recommended for pastures in eastern Canada. Objectives were to evaluate the potential of KC when grown in mixtures with grasses and compare its performance with WC based‐mixtures and N‐fertilized grass monocultures. Twenty treatments that included KC, WC, and six perennial grasses species (Kentucky bluegrass [Poa pratensis L.; KB], meadow bromegrass [Bromus biebersteinii Roem. & Schult., MB], orchardgrass [Dactylis glomerata L., OR], smooth bromegrass [Bromus inermis L.; SB], tall fescue [Schedonorus arundinaceus (Schreb.) Dumort.; TF], and timothy [Phleum pratense L.; TI]) seeded alone and in binary mixtures were seeded in 2 yr at two sites and monitored for up to four production years. During the first production year, WC‐based mixtures yields were overall greater than those of KC‐based mixtures, while in the second production year and onwards, KC treatments had similar or greater yields than WC, illustrating the greater persistence of KC. Adding KC to grasses also increased total forage yields by 13% on average compared to N‐fertilized solo‐seeded grasses. The performance of specific KC–grass mixtures was variable across sites‐years with no specific mixture being consistently more productive. Kura clover is adapted to contrasting environments of Québec and appears to be a suitable alternative to WC. [ABSTRACT FROM AUTHOR]

Abstract Other than from its sensing and processing capabilities, a mobile robotic platform can be limited in its use by its ability to move in the environment. Legs, tracks and wheels are all efficient means of ground locomotion that are most suitable in different situations. Legs allow to climb over obstacles and change the height of the robot, modifying its viewpoint of the world. Tracks are efficient on uneven terrains or on soft surfaces (snow, mud, etc.), while wheels are optimal on flat surfaces. Our objective is to work on a new concept capable of combining different locomotion mechanisms to increase the locomotion capabilities of the robotic platform. The design we came up with, called AZIMUT, is symmetrical and is made of four independent leg-track-wheel articulations. It can move with its articulations up, down or straight, allowing the robot to deal with three-dimensional environments. AZIMUT is also capable of moving sideways without changing its orientation, making it omnidirectional. By putting sensors on these articulations, the robot can also actively perceive its environment by changing the orientation of its articulations. Designing a robot with such capabilities requires addressing difficult design compromises, with measurable impacts seen only after integrating all of the components together. Modularity at the structural, hardware and embedded software levels, all considered concurrently in an iterative design process, reveals to be key in the design of sophisticated mobile robotic platforms. [ABSTRACT FROM AUTHOR]