Quantitative PCR (qPCR) has become the gold standard technique to measure cDNA and gDNA levels but the resulting data can be highly variable, artifactual and non-reproducible without appropriate ...verification and validation of both samples and primers. The root cause of poor quality data is typically associated with inadequate dilution of residual protein and chemical contaminants that variably inhibit Taq polymerase and primer annealing. The most susceptible, frustrating and often most interesting samples are those containing low abundant targets with small expression differences of 2-fold or lower. Here, Droplet Digital PCR (ddPCR) and qPCR platforms were directly compared for gene expression analysis using low amounts of purified, synthetic DNA in well characterized samples under identical reaction conditions. We conclude that for sample/target combinations with low levels of nucleic acids (Cq ≥ 29) and/or variable amounts of chemical and protein contaminants, ddPCR technology will produce more precise, reproducible and statistically significant results required for publication quality data. A stepwise methodology is also described to choose between these complimentary technologies to obtain the best results for any experiment.
Fungi play important roles in forest ecosystems and understanding fungal diversity is crucial to address essential questions about species conservation and ecosystems management. Changes in fungal ...diversity can have severe impacts on ecosystem functionality. Unfortunately, little is known about fungal diversity in northern temperate and boreal forests, and we have yet to understand how abiotic variables shape fungal richness and composition. Our objectives were to make an overview of the fungal richness and the community composition in the region and identify their major abiotic drivers. We sampled 262 stands across the northern temperate and boreal Quebec forest located in the region of Abitibi-Témiscamingue, Mauricie, and Haute-Mauricie. At each site, we characterized fungal composition using Illumina sequencing, as well as several potential abiotic drivers (e.g., humus thickness, soil pH, vegetation cover, etc.). We tested effects of abiotic drivers on species richness using generalized linear models, while difference in fungal composition between stands was analyzed with permutational multivariate analysis of variance and beta-diversity partitioning analyses. Fungi from the order Agaricales, Helotiales, and Russulales were the most frequent and sites from the north of Abitibi-Témiscamingue showed the highest OTUs (Operational Taxonomic Unit) richness. Stand age and moss cover were the best predictors of fungal richness. On the other hand, the strongest drivers of fungal community structure were soil pH, average cumulative precipitation, and stand age, although much of community variance was left unexplained in our models. Overall, our regional metacommunity was characterized by high turnover rate, even when rare OTUs were removed. This may indicate strong environmental filtering by several unmeasured abiotic filters, or stronger than expected dispersal limitations in soil fungal communities. Our results show how difficult it can be to predict fungal community assembly even with high replication and efforts to include several biologically relevant explanatory variables.
Boreal forests provide important ecosystem services, most notably being the mitigation of increasing atmospheric CO2 emissions. Microbial biodiversity, particularly the local diversity of fungi, has ...been shown to promote multiple functions of the boreal forests of Northeastern China. However, this microbial biodiversity-multifunctionality relationship has yet to be explored in Northeastern Canada, where historical environment have shaped a different regional pool of microbial diversity. This study focuses on the relationship between the soil microbiome and ecosystem multifunctionality, as well as the influence of pH and redox potential (Eh) on the regulation of such relationship. Structural equation modelling (SEM) was used to explore the different causal relationships existing in the studied ecosystems. In a managed part of the Canadian boreal forest, 156 forest polygons were sampled to (1) estimate the α- and β-diversity of fungal and bacterial communities and (2) measure 12 ecosystem functions mainly related to soil nutrient storage and cycling. Both bacteria and fungi influenced ecosystem multifunctionality, but on their own respective functions. Bacterial β-diversity was the most important factor increasing primary productivity and soil microbial biomass, while reducing soil emitted atmospheric CO2. Environmental characteristics, particularly low levels of organic matter in soil, were shown to have the strongest positive impact on boreal ecosystem multifunctionality. Overall, our results were consistent with those obtained in Northeastern China; however, some differences need to be further explored especially considering the history of forest management in Northeastern Canada.
Background: Wild edible mushroom harvesting is a booming activity in Canada, mostly in Quebec, Ontario, and British Columbia. This increasing demand requires pickers to find more picking areas. ...However, several challenges are encountered, making fungal inventory difficult to achieve: (i) mushrooms are only available during a short period of the year, (ii) their abundance varies from year-to-year according to environmental conditions, and (iii) only the fructifications are visible. In order to assess the fungal presence of an area, we propose to use environmental metabarcoding combined with next-generation sequencing methods on soil samples. Results: The first step of this study was to construct a local DNA barcode reference library for Canadian fungi using a selection of 32 edible species (commercial interest) to be included in a probabilistic presence model. In total, 107 barcodes spanning the entire ITS (Internal Transcribed Spacer) region were obtained from local samples. Soil samples taken from 300 sites, selected among 33 000 sites across the province of Quebec (Canada) that have been characterized by 75 ecological parameters, were sequenced by Illumina MiSeq for the ITS1 and ITS2 region. The metabarcoding data obtained represent the total fungal biodiversity of each site (not only the selected species), and they were combined with ecological parameters to calibrate and generate a mathematical model that can be projected to the 33 000 inventory sites. Presence probability maps have been generated that indicate potential new areas to find the studied species. Significance: This is the first effort to use metabarcoding to characterize the fungal biodiversity of soil samples in the province of Quebec and also to conceive a mathematical model to predict the presence of mycelium. It will also provide a key tool to mushroom pickers to facilitate their research across the vast territory of Quebec.
Lobster mushroom is a wild edible mushroom with potential commercial value. It is the product resulting of the infection, most commonly of Russula brevipes, by Hypomyces lactifluorum. This study ...undertook quantitative polymerase chain reaction analysis of tissues sampled at different infection stages to investigate R. brevipes – H. lactifluorum interaction. We followed the colonization of R. brevipes sporocarps by H. lactifluorum that leads to the edible lobster mushrooms. In parallel, metabolomics analysis was performed to detect differences in metabolite profile among non-infected R. brevipes sporocarp and lobster mushroom. The results show that H. lactifluorum DNA is not restricted to the margin but is distributed relatively evenly across the sporocarp of the lobster mushroom. Russula brevipes DNA was also present throughout the sporocarp but was less abundant at the margins and increased inwards. Russula brevipes DNA also declined as the infection progressed. Metabolomics analysis revealed that the flesh of lobster mushroom, which remains identical in appearance to the flesh of the host, undergoes transformation that alters its metabolite profile, most notably of lipids and terpene compounds. These results define a parasitic relationship between the two species that entails a decline of R. brevipes DNA and a modification of its metabolite profile.
The purpose of this paper is to explore the potentiel of the egg as a primary material in a creative and therapeutic process. My research is introduced by an historical study of the use of the egg as ...a daily object as well as an art object. We will discover, on a folk and sacred level, the myths, customs, traditions and beliefs related to different cultures. We will study the physical and symbolical structure of the egg by comparing it to the cell, the body, the language and the atom as well as studying its symbolical and analogical values. We will briefly look at the theory of Guillaume and Bohr that will support the hypothesis that the egg incarnates creation as well as mystery. A last part of my research includes a personal research centered on the artistic exploration of the egg as a primary matter. This will allow the understanding and the integration of the essence of the creative processes put in perspective with images that reveal the dynamics that the egg engenders
Aims
To shed light on the process of advocacy in the context of community health nursing, through a methodology inspired by the epistemologies of the South.
Design
We conducted a collaborative ...ethnography in a community health centre in Canada.
Methods
de Sousa Santos' epistemologies of the South, a typology of advocacy and main themes from historic research informed the methodology. Data were collected between 2016 and 2018 through 420 h of fieldwork observations and three group discussions, including a collective process to co‐construct interpretations with participants. Twenty‐one nurses participated in the study.
Results
Nurses had sufficient work flexibility to practice advocacy actions focused on individuals and groups. They also engaged in attempts at policy reform in the form of defending access to appropriate care and changing the mode of care organization. However, these were curbed by bureaucracy and administrative rules, resulting in the eventual dismissal of health promotion actions and experiences of moral distress.
Conclusion
Despite the political climate of their work environment impeding social justice agendas, nurses' advocacy practices showed a persistence of moral values and ideals in coherence with the regional nursing legacy.
Implications for the Profession and/or Patient Care
Acting at the organizational level and involving field nurses in decision making are potential avenues for increasing policy advocacy efficacy.
Impact
Examining contexts through another epistemic lens and methods of research drawing on history and anthropology has shed light on a process of advocacy. This research shows that organizations need to equip themselves with mechanisms to promote the sharing of realities between nurses, thereby building collective advocacy.
Reporting Method
The research adheres to the EQUATOR guidelines with SRQR and COREQ methods.
Patient or Public Contribution
No patient or public contribution.
Stereotactic radiosurgery (SRS) is offered to patients for recurrent brain metastases after prior brain radiation therapy (RT), but few studies have evaluated the efficacy of salvage SRS or factors ...to consider in selecting patients for this treatment. This study reports overall survival (OS), intracranial progression-free survival (PFS), and local control (LC) after salvage SRS, and factors associated with outcomes.
This is a retrospective review of patients treated from 2009 to 2011 with salvage SRS after prior brain RT for brain metastases. Survival from salvage SRS and from initial brain metastases diagnosis (IBMD) was calculated. Univariate and multivariable (MVA) analyses included age, performance status, recursive partitioning analysis (RPA) class, extracranial disease control, and time from initial RT to salvage SRS.
There were 106 patients included in the analysis with a median age of 56.9 years (range 32.5-82 years). A median of 2 metastases were treated per patient (range, 1-12) with a median dose of 21 Gy (range, 12-24) prescribed to the 50% isodose. With a median follow-up of 10.5 months (range, 0.1-68.2), LC was 82.8%, 60.1%, and 46.8% at 6 months, 1 year, and 3 years, respectively. Median PFS was 6.2 months (95% confidence interval CI = 4.9-7.6). Median OS was 11.7 months (95% CI = 8.1-13) from salvage SRS, and 22.1 months from IBMD (95% CI = 18.4-26.8). On MVA, age (P=.01; hazard ratio HR = 1.04; 95% CI = 1.01-1.07), extracranial disease control (P=.004; HR = 0.46; 95% CI = 0.27-0.78), and interval from initial RT to salvage SRS of at least 265 days (P=.001; HR = 2.46; 95% CI = 1.47-4.09) were predictive of OS.
This study demonstrates that patients can have durable local control and survival after salvage SRS for recurrent brain metastases. In particular, younger patients with controlled extracranial disease and a durable response to initial brain RT are likely to benefit from salvage SRS.
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