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Using amplicon and primer tiling to define the target regions of commercial nucleic acid amplification tests for SARS-COV-2 detection
No full textThe novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus is the causative agent of the coronavirus disease-19 (COVID-19) pandemic, that has caused economic collapse and millions of deaths world-wide. During the pandemic, molecular surveillance became imperative as it not only provided key information such as, pathogenicity, transmission, circulation and evolution of the virus, but was also used to ensure quality assurance diagnostics. As nucleic acid amplification tests (NAATs) were the primary method for SARS-CoV-2 detection, sequence mismatches between circulating SARS-CoV-2 strains and NAAT target sites can lead to reduced sensitivity and diagnostic failure. Thankfully, using bioinformatics, primer/probe sequences used in NAATs can be compared to published SARS-CoV-2 genomic data to identify any discrepancies. Unfortunately, due to the proprietary nature of commercial tests, this can only be done for laboratory developed tests (LDTs). In order to define areas to monitor in subsequent mutations analyses, this study aimed to define the precise genomic locations of target genes (i.e., E and N2) used in a commonly used commercial NAAT, the Xpert Xpress' SARS-CoV-2. First, amplicons produced from reverse transcription polymerase chain reactions (RT-PCR) using overlapping primer pairs (i.e., amplicon tiling) spanning E and N2 genes were subjected to Xpert assay, to estimate the target regions. To further refine the minimal area required for Xpert positivity, additional various combinations of overlapping forward and reverse primers (i.e., primer tiling) were used within the area identified by amplicon tiling. Primer yielding positive results were aligned to a reference genome to identify primer locations. Altogether, the target regions for the Xpert E and N2 genes were estimated between 26269 to 26381 and 29164 to 29230, respectively. These regions were confirmed with next-generation sequencing using amplicons retrieved from an Xpert reaction tested ion a positive clinical specimen. Based on our results, amplicon and primer
tiling proves to be a sequencing-independent technique to estimate the genomic location of undisclosed commercial assay targets. Paired with a method of mutation assessment, this would provide a framework for the maintenance of quality assurance in clinical diagnostic testing and
could be applied to SARS-CoV-2 assays, as well as any molecular method
Mercury photochemistry and speciation in the Jijuktu'kwejk (Cornwallis River) estuary of the Minas Basin, Nova Scotia
No full textThe photochemistry and speciation of mercury are important factors in the retention of mercury in estuarine ecosystems. Net photoreduction of divalent mercury (Hg(II)) and volatilization of photoreduction products (i.e., elemental mercury (Hg(0))/dissolved gaseous mercury (DGM) can be a mechanism by which mercury burdens in ecosystems are decreased and thereby bioaccumulation and biomagnification could be decreased. The interaction of salinity and dissolved organic matter (DOM) and the potential influence on mercury photoreactions is not well understood. Anions may compete with DOM for binding sites on Hg(II), and cations may compete with Hg(II) for binding sites on DOM. The effects of salinity were investigated while controlling the concentration of high molecular weight (>1 kDa) DOM using natural surface water from the tidal Jijuktu'kwejk (Cornwallis River) using a tangential ultrafiltration-dilution technique. Pseudo first-order rate constants in estuarine water dilutions ranged between 0.22 h-1 and 0.73 h-1. The amount of mercury available for photoreduction in the dilutions (Hg(II)RED) ranged between 67.25 pg and 265.91 pg. Pseudo first-order rate constant was found to decrease with increasing salinity, with lower salinity solutions (57% loss), suggesting a loss of DOM reactivity. In a separate field experiment, mercury photoreactions were quantified in a tidal river by measuring dissolved and particulate mercury species concurrently with incoming solar radiation intensity, TSS, DOM, and salinity every 0.5 hours during daylight hours. Hg(0)aq concentration was not correlated with incoming radiation intensity, but was negatively correlated with TSS, suggesting radiation penetration is limited by TSS. Overall, photoproduction of Hg(0)aq appears to be highly suppressed by TSS limiting transmission of UV radiation through surface waters. This is demonstrated by the large amount of Hg(0) production in controlled lab experiments with filtered surface water in comparison to field measurements using unfiltered samples, Hg(0)aq concentrations in unfiltered surface water were largely nondetectable (0–12 pg L-1) in the presence of high ERM concentrations in filtered surface water (mean=147 pg L-1, SD=104 pg L-1). This thesis highlights the importance of salinity and DOM interactions in estuarine surface water and their effects on mercury photochemistry. It also demonstrates the importance of complementary laboratory and field measurements in mercury photochemistry research
Terpene classification using mass spectra data and machine learning
No full textTraditionally, separation and classification of terpenes from food samples is done with thehelp of two processes, namely: Gas Chromatography (GC) (separate terpenes from each other) and Mass Spectrometry (MS) (detects the separated terpenes). A mass spectrum is matched to known terpenes by a chemist using an existing database of various samples. We propose a machine learning solution that detects multiple terpenes from mass spectra without separating them. Synthetic data is generated using six common terpenes, cannabid-iol (CBD) and tetrahydrocannabinol (THC) using an additive composition model with five percent resolution in each component. The six base terpenes included in the current study are myrcene, linalool, limonene, α-pinene, β-pinene, and trans-caryophyllene, referred to as target chemicals. These terpenes are found in many food products that we consume in our day-to-day lives. There are 50,388 possible mass spectra combinations of these terpenes. The research investigates the development of a machine learning approach that classifies and quantifies the target chemicals. The system reads the mass spectra and automatically detects target chemicals that are present and determines their relative proportions. Various supervised and unsupervised classification and regression models are built and tested.Principal Component Analysis (PCA) of the eight target chemicals is performed to test how distinguishable the terpenes are. Classification of the major contributor target chemical with the help of artificial neural networks and a deep learning algorithm results in an accuracy of 99.1% for target chemicals respectively based on a train-test split methodology. Regression results with the help of ANNs and a single-layered model result in a mean absolute error of 0.001222 for target chemicals based on a train-test split methodology
Overparenting, adult attachment styles, and caregiver attitudes while raising a virtual child
No full textThe present study examined the relationship between overparenting behaviours, adult attachment styles, and caregiver attitudes developed while raising a virtual child. 117 students registered in developmental psychology courses participated in an online survey administered through LimeSurvey. Participants completed measures of overparenting behaviours and attachment styles at Time 1 before raising their child to 18 years old using the MyVirtualChild© program, and the same measures after rising their child at Time 2 in addition to measures of caregivers' attitudes towards the child. For the attachment styles, anxiety and avoidance were found to be negatively related to caregiver attitudes, and hierarchal regressions showed avoidance, but not anxiety, was a negative predictor of the positive caregiver attitudes of perceived child security and willingness to serve as an attachment figure, but not positive feelings towards the child. Overparenting from the participant's own mother was positively related to anxious attachment style and how they saw themselves as overparenting parents was negatively related to avoidance, but not anxiety. Overparenting measures did not predict caregiver attitudes. The present study's findings show avoidance in adult attachment styles, but not overparenting, predicts caregiver attitudes even when raising a virtual child in a simulated parenting experience
Individual differences in attention: autism traits and attachment styles as moderators of holistic processing of faces and objects
No full textThe present study examined whether attachment styles and traits associated with autism spectrum disorder (ASD) moderate holistic processing of face and non-face objects. The literature reveals greater levels of face and object holistic processing are associated with greater experience (e.g., Bukach et al., 2010). However, lower levels of holistic processing have been reported in persons with ASD for both faces and objects (e.g., Dawson et al., 2005), and these effects have been associated with variations in attention styles related to attachment (e.g., Dykas & Cassidy, 2011). We hypothesized that holistic processing of faces and objects may be predicted by levels of autism traits and that attachment styles would moderate this relationship. A sample of 158 undergraduate participants completed the Vanderbilt Holistic Processing Test for Faces (VHPT-F; Richler et al., 2014) and the Vanderbilt Holistic Processing Test for Novel Objects (VHPT-NO; Chua & Gauthier, 2020a) to measure individual differences in holistic processing. Social Measures included the Autism-Spectrum Quotient (AQ; Baron-Cohen et al., 2001) to measure autism traits and the Experiences in Close Relationships-Short Form (ECR- SF; Wei et al., 2007) to evaluate adult attachment style. Holistic processing was associated with attachment styles and autism traits, but only for objects. These results of this study were consistent with the expertise hypothesis of holistic processing (e.g., Diamond & Carey, 1986), and the argument that individual differences in characteristics are related to holistic processing (e.g., Gauthier, 2020), but these findings were only observed for objects and not for faces
Characterization of Long's Braya (Braya longii) and Brassicacae volatiles and oviposition preference of the Diamondback moth (Plutella xylostella)
No full textLong's Braya (Braya longii) is a member of the Brassicaceae family and an endangered plant species found only in the Northern Peninsula of Newfoundland. Every year, B. longii is subject to infestations of the diamondback moth (Plutella xylostella), wherein their larvae consume and eventually kill B. longii. Around the world, P. xylostella is a notorious agricultural pest that is difficult to manage due to its resistance to both chemical and biological insecticides. In this study, volatile organic compounds (VOCs) of B. longii and other members of the Brassicaceae were collected and their composition were analysed. Volatile compositions from previous studies of Brassica spp. were also compared with B. longii to identify key compounds that may cause behavioural attraction in P. xylostella. Afterwards, P. xylostella were subject to these host plant volatiles as well as individual key compounds using Gas Chromatography
coupled with Electroantennographic Detection (GC-EAD), Electroantennography (EAG) and oviposition assays to study antennal responses and egg-laying behaviour. A putative attractive compound eliciting an antennal response in P. xylostella identified from broccoli and rutabaga GC-EAD trials was 1-undecanol, however positive identification remains to be conducted through comparison with analytical standards on Gas Chromatography Mass Spectrometry (GC-MS). Compounds chosen for EAG screenings were hexanal, octanal, nonanal, ethyl palmitate, 1-octanol and (Z)-3-hexenol, and were diluted to 10 ng/μL-10 μg/μL concentrations. We found that (Z)-3-hexenol, octanal and 1-octanol at concentrations of 1 and 10 μg/μL elicited antennal responses in P. xylostella during EAG recordings. Afterwards, octanal, nonanal and (Z)-3-hexenol were selected for behavioural assays. We noted that P. xylostella was more attracted to
(Z)-3-hexenol treated radish at 10 μg at oviposition sites. However, there was no preference to either control or treatment when lures were raised to 100 μg loads. EAG screening found differences in antennal responses to key alkanals. While octanal and nonanal elicited antennal responses, they did not provide any significant behavioural preference for either control or treatment. The data collected from this study provides electrophysiological and behavioural responses of P. xylostella to VOCs emitted from Braya longii and Brassica host plants. Future studies should replicate GC-EAD trials and provide a definite identification of potential key compounds so a host-finding mechanism can be found. This knowledge could then be used to develop novel tools for the pest management of P. xylostella
Kaleidoscope
No full textThis creative writing thesis is a collection of six short stories entitled Kaleidoscope, a title chosen to reflect the multiplicity and fractal nature of the collection and the genres represented therein; each story is both a whole and a fragment, reflecting and refracting off one another. Each of the six stories explores a different kind of contemporary genre-fiction as popularly conceived, namely comedy, romance, horror, mystery, fantasy, and sci-fi. These six were selected because of their continued prevalence in genre-fiction over the past century, as well as the overlapping differences and similarities which become apparent when offset against one another.
Though "genre" as a concept is both complex and expansive, this thesis attempts to reveal how and why the formulas of popular genre-fiction endure, despite being perceived as lesser than "literary fiction." The distinction between high and low art is being blurred with the progress of cultural and literary studies and the hierarchy of genres has been overturned. The formulas of conventional genre-fiction have been and continue to be endlessly repeated and endlessly appealing with patterns that stand the test of time. The aim of this collection is not to define genre, or to define the genres of each story, as the concept of genre is so nebulous and contested that this task would be near impossible; rather the aim is to imitate, vary, and innovate upon the starting point of familiar tropes and conventions of each genre to create six unique and compelling stories. Each story stands on its own as an imitation of a well-loved example of genre-fiction, creating variations upon these established traditions, and providing innovative elements to bolster the enjoyment and satisfaction of the reader, thereby creating a dream from which no reader would wish to wake
Functionalization of carbon dioxide through the use of amino phosphonates
No full textThe culminating effect of increasing greenhouse gasses on climate change has proven to be a significant scientific concern. Due to its increased concentration and long decay time, carbon dioxide is responsible for nearly half of the greenhouse effect. The main contributor responsible for carbon dioxide emissions comes from fossil fuels, which accounts for 75% of all anthropogenic carbon dioxide emissions. It would be impractical to halt the use of fossil fuels as they contribute to 86% of the entire world's energy and can be found in nearly every region of the globe. There in lies the urgency to determine a way to capture and/or utilize the carbon dioxide in the atmosphere. Alkyl and aryl phosphonates were evaluated in multiple fashions with the interest of attaching an amino group to each substituent of the phosphonates. The synthesis of bis(2-aminoethyl) phosphonate was attempted through the heat reaction, HCl method, modified HCl method, acetic acid method, and the base solution method, with partial success only in the acetic acid reaction using diphenyl phosphonate. Control carbamates were tested for carbon capture capabilities by testing a multitude of solvents with 2-aminoethanol at room temperature and 38 °C. Absolute and 95% ethanol solvents both resulted in captured carbon dioxide by 2-aminoethanol
Preliminary comparative analysis of SOX9, KRAS, TP53, APC and SMAD4 gene expression in colorectal patients from the cancer genome atlas -- Firehose legacy study
No full textThe Canadian Cancer Society reports colorectal cancer (CRC) remains the second highest cause of cancer mortality in men and the third in women. Genetic mutations play a fundamental role in the formation and development of cancer. Mutation of several proto-oncogenes and tumor suppressor genes involved in key signal transduction pathways have proposed to play a crucial role in the initiation of cancer. In this study, a collection of colorectal cancer patient samples from The Cancer Genome Atlas (TCGA) Firehose legacy were analyzed. Clinical and mRNA expression data were attained from cBioportal. Gene expression of five genes of interest in colorectal cancer were analyzed, SRY-Box transcription factor-9 (SOX9), Kristen rat sarcoma virus (KRAS), adenomatous polyposis coli (APC), tumor protein gene 53 (TP53), and SMAD family member 4 (SMAD4). Sample data were divided based on clinical differences in survival status, sex, and progression stage. The gene expression of each gene of interest were compared to identify any significant differences in expression between different clinical groups. Tumor suppressor APC displayed a significant difference in mRNA expression between male and female colorectal (CRC) patient groups. Tumor suppressor SMAD4 was significantly downregulated between stage I and IV CRC patient samples and stage II and IV CRC patient samples. Downregulation of APC in males supports the high incidence of CRC in males. APC's involvement in the WNT signaling pathway suggests this pathway is likely disrupted in CRC and play a significant role in the CRC development and progression. SMAD4's implication in TGF-β suggests a disruption of this cellular signaling pathway. WNT and TGF-β signaling pathways may therefore be of interest for future research to better understand cancer at a genetic and cellular level. APC and SMAD4 may provide useful intracellular therapeutic targets, or act as potential biomarkers for CRC
Behavioural and neural effects of caffeine on cognition in hormonally cycling females
No full textThe present study examined behavioural and neurophysiological effects of caffeine on cognition across menstrual cycle phases. Sixty healthy females with hormonally-mediated menstrual cycles (i.e. using combination oral contraceptives) between the ages of 18-40 participated in a double-blind, placebo-controlled, randomized study. Participants were tested during their menstrual or combination hormonal
contraceptive (HC) active cycle phase. Saliva hormone testing was used to confirm menstrual cycle phase. Participants took a caffeine or placebo pill in counterbalanced order before the completion of a visual search task while EEG was recorded. ANCOVAs were used to examine the effects of menstrual phase and drug on behavioural (RT, accuracy) and neurophysiological (amplitude, latency of ERP waveforms previously elicited in visual search tasks; the N2pc and P300) outcome measures. Spearman's rho was used to examine correlations between hormone levels and caffeine-induced changes for outcome measures. Behavioural results revealed that caffeine improved accuracy but slowed reaction time to targets in the combination HC active phase only. EEG results showed no phase or drug effects on P300 outcome measures. In the caffeine condition, N2pc amplitudes at the parietal occipital region to distractor arrays were significantly larger compared to the placebo condition; this pattern reversed for target arrays. These results suggest a potential reallocation of attention from target to distractor stimuli during the combination HC active cycle phase to maintain task efficiency. Findings contribute to a better understanding of the neurocognitive mechanisms underlying the effects of caffeine on cognition across menstrual cycle phases, which have implications for hormonal birth control as well as hormone therapies for transgender and post-menopausal women