McGill Science undergraduate research journal : MSURJ最新文献_第3页

Comparison of Small Molecule-Responsive RNA Aptazymes for Applications in Gene Control 小分子反应性RNA适配酶在基因控制中的应用比较

McGill Science undergraduate research journal : MSURJ Pub Date : 2022-03-26 DOI: 10.26443/msurj.v18i1.191

Janeva Shahi, M. McKeague

{"title":"Comparison of Small Molecule-Responsive RNA Aptazymes for Applications in Gene Control","authors":"Janeva Shahi, M. McKeague","doi":"10.26443/msurj.v18i1.191","DOIUrl":"https://doi.org/10.26443/msurj.v18i1.191","url":null,"abstract":"Modelling how genes act in both space and time is critical to understand animal development, which can potentially drive intervention in gene expression. Gene regulation is examined using many techniques; however, challenges such as cell delivery, invasiveness, toxicity, and efficacy limit our ability to fully probe gene networks. Recent advances have led to the development of tunable, titratable, and reversible tools that can be genetically-encoded into animal model systems to modulate genes with temporal and spatial control. This study compares such tools, testing several aptazyme-based switches that can be expressed inside cells and controlled through the addition of non-toxic small molecules. Three switches responsive to different small molecules were compared for switching activity in mammalian cells. The most efficient switches in terms of activity gauged by their modulation of gene expression were then further assayed. Finally, the specificity of the hypoxanthine switch was tested based on chemical structure and classification. The comparisons revealed the importance of both timing and small molecule concentrations on switch activity, while the specificity testing demonstrated switch activity inside the cell correlated to the aptamer binding properties that were measured biochemically. This work demonstrates the suitability of aptazyme-based switches for application in diverse genetic environments, and in controlling and studying gene networks in animals. ","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42750192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative analysis of delivery methods for stem cell therapy in liver diseases 肝脏疾病干细胞治疗递送方法的比较分析

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.65

Zhiyue Zhu

{"title":"Comparative analysis of delivery methods for stem cell therapy in liver diseases","authors":"Zhiyue Zhu","doi":"10.26443/msurj.v16i1.65","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.65","url":null,"abstract":"Background: Mesenchymal stem cell transplantation is an emerging therapy for treating acute and chronic liver diseases as an alternative for patients who are not transplant candidates. The potential of this treatment depends on its therapeutic efficiency and safety, which have been investigated and evaluated in both preclinical and clinical settings. However, there are still some risks associated with the delivery methods, such as low long-term retention rate and the possibility of arousing cancer or rejection.\u0000Methods: During the review process, previous papers mentioning “stem cell treatment” and “liver diseases” were searched. We described different up-to-date approaches for stem cells from various origins to be delivered to the liver and compared respectively their pros and cons for clinical applications. We also proposed several potential techniques for future studies.\u0000Summary: An efficient and safe stem cell delivery could be enabled via Alginate-Polylysine-Alginate (APA) microencapsulation, lipid-conjugated coating or the use of nanoparticles. Their efficacy will be improved through tissue engineering and microrobots as the delivery is sustained and targeted with fewer rejection responses.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44916534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Role of Stress in the Spread of Transposable Elements 应力在转座因子传播中的作用

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.63

Oscar Dumoulin

{"title":"Role of Stress in the Spread of Transposable Elements","authors":"Oscar Dumoulin","doi":"10.26443/msurj.v16i1.63","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.63","url":null,"abstract":"Background: Transposable elements (TEs) and genomes have been at war for millions of years. On one hand, genomes developed epigenetic systems to inactivate TEs. On the other hand, it appears that TEs can take advantage of stress to evade the genome’s repressing systems and spread throughout the genome. However, until recently it was unclear how and why stress influences transposable elements’ movement. In this review, we explore the mechanisms involved in TE stress-induced activation.\u0000Methods: The first part of the review looks into epigenetic mechanisms, its 19 references were taken from Handbook of Epigenetics 2nd edition (1) and reviews (2) (3). The rest of the studies presented in this review were drawn from searches done on Web of Science with the terms: TS=((Transposable element* OR mobile genetic element*) AND (Stress or Evolution) AND (Activation)) with peer-reviewed articles and reviews written in English included only. The search yielded 401 results and 56 were estimated relevant and of sufficient quality to be selected.\u0000Summary: The main conclusion reached by this review is that protection mechanisms against TEs movement, which are mostly epigenetic, are compromised by the presence of stress. Additionally, TEs themselves evolved diverse tools to promote their activation under certain stress conditions allowing them to evade the repression imposed by the genome. These two mechanisms provide opportunities for TEs to move around the genome and create genetic diversity during stress episodes. As such, TEs stress induced mobility certainly played a major role in the rapid adaption of populations and its impact can be witnessed across genomes.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45161331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Imagine All the People: Investigating People’s Perceptual Biases as They Pertain to Age, Race, and Gender 想象所有的人:调查人们的感知偏见，因为他们与年龄，种族和性别有关

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.55

Marie-Louise E. Audet

{"title":"Imagine All the People: Investigating People’s Perceptual Biases as They Pertain to Age, Race, and Gender","authors":"Marie-Louise E. Audet","doi":"10.26443/msurj.v16i1.55","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.55","url":null,"abstract":"Typically, perceptual biases are studied by investigating how people respond to written scenarios, without considering the mental representations people form while reading these descriptions. This paper provides a novel approach to face perception research by looking at people’s mental representations of strangers and aims to determine whether current ways of classifying people into definite race, age, and gender categories were accurate or needed to be rethought. Specifically, participants digitally reproduced the faces they imagined while reading different scenarios where strangers were described only by race, age, and gender (N = 76). Subsequently, a different set of participants rated these faces on various traits (N = 1024). In the first part of the study, participants created 9 faces from written descriptions of strangers, the last of which included information about criminal history. In the second part, participants rated these faces on dimensions of attractiveness, trustworthiness, intelligence, and physical strength for faces in the non-crime condition, and on dimensions of threat, criminality, and attractiveness for the crime condition. Linear regression models showed that age, race, and gender had various effects on scores on different dimensions, as well as on within-group variance. For instance, older faces were awarded lower attractiveness ratings than younger faces overall, an effect which was also moderated by race, with older age being less predictive of attractiveness ratings for Black faces. Furthermore, there was significantly less variability in attractiveness ratings for Black faces than White faces. Overall, this study revealed that stereotypes do not always adhere to clear-cut categories of race, age, and gender, suggesting that they may be applied somewhat dimensionally rather than categorically.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47418379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Automated ultrasonic vocalization analysis: Training and testing VocalMat on a rat-based dataset 自动超声波发声分析:在基于老鼠的数据集上训练和测试VocalMat

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.58

Samir Gouin

{"title":"Automated ultrasonic vocalization analysis: Training and testing VocalMat on a rat-based dataset","authors":"Samir Gouin","doi":"10.26443/msurj.v16i1.58","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.58","url":null,"abstract":"Background: Ultrasonic vocalizations (USVs) offer another way to study the behaviour of rodents in addition to commonly used visual methods. USV subtypes have been associated with behaviour such as the concurrence of 22-kHz calls and signs of distress (defensive behaviour). (1,2) However, the categories used to analyze USVs are a source of contention, most notably with 50-kHz calls, and may even be arbitrary altogether. (3) To facilitate subtyping calls, VocalMat has been developed for USV identification and classification, and it has shown an accuracy of greater than 98% for mice USV detection and 86% for mice USV classification. (4) In this project, we have constructed a rat-based dataset of USVs and then used it to train the VocalMat program to assess automated USV classification.\u0000Methods: Avisoft-SASLab Pro was used to manually classify USVs from 216 audio files. The sorted USVs were then used to train VocalMat’s classification program.\u0000Results: Our results show overall accuracies greater than 90% with the highest in the trill and flat categories (97.2% and 91.0%). We experimented with the number of USV categories and found high accuracies when grouping spectrographically similar calls, which are flat calls with up and down ramp calls (96.9%) and trill calls with trill jump and flat-trill calls (98.7%).\u0000Limitations: There are large variations in the number of calls per category in our dataset. More data is needed to fill these gaps and provide more training samples for infrequent calls.\u0000Conclusions: By creating a database of rat USVs and then using it to train VocalMat, we have shown the potential of its adaption to a rat vocal repertoire. Going forward, we hope to test more variations of USV categories on machine learning programs to establish a robust approach to classifying USVs.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49131119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

What is the Best Music for Neurofeedback Training? 什么是神经反馈训练的最佳音乐？

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.59

Lyla Hawari, N. Singer, Arielle G. Rabinowitz, R. Zatorre

{"title":"What is the Best Music for Neurofeedback Training?","authors":"Lyla Hawari, N. Singer, Arielle G. Rabinowitz, R. Zatorre","doi":"10.26443/msurj.v16i1.59","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.59","url":null,"abstract":"The nucleus accumbens (NAc) is widely known for its role in reward seeking behavior which is heavily reliant on dopamine signaling. Dopamine plays an important role in reward seeking behavior and motivation and its dysregulation is shown to cause symptoms of depression such as apathy, a lack of motivation, and anhedonia, a loss of pleasure. Studying the NAc, specifically the ventral striatum in this case, is critical in understanding the underlying mechanisms of this dysregulation. Music neurofeedback is a biofeedback technique that provides feedback on brain activity through the audio quality of the music, with lower quality sounding more muffled. This study uses this technique to train participants to increase the activity of their ventral striatum in an attempt to upregulate the activity of the reward system. \u0000This paper aims to investigate what the most effective music choices are in terms of genre, key, valence (positive or negative emotions) and energy (pertaining to levels of arousal) to maximize the improvement on neurofeedback training. These musical attributes were identified by the Spotify “Organize Your Music” categorization tool. Participants underwent six EEG music neurofeedback training sessions with individually tailored pleasurable music as the source of feedback. The participants either received real feedback in the neurofeedback group (NF) or sham feedback in the control group. The results of this study showed that neurofeedback performance was negatively correlated with valence whereby songs that led to the greatest performance, measured as increase in ventral striatum activity from baseline, were those low in valence. Participants that had the greatest improvement in their neurofeedback training selected songs that were in a minor key and belonged to the pop genre. Although this study is based on a small sample, it takes the first step towards the overarching goal of using music to manage dysregulation in the reward system.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45320762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Design and evaluation of small interfering RNAs for the treatment of Severe Acute Respiratory Syndrome-Coronavirus-2 小干扰RNA治疗严重急性呼吸综合征冠状病毒2型的设计与评价

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.62

William Zhang, A. Daher, A. Gatignol, Robert J. Scarborough

{"title":"Design and evaluation of small interfering RNAs for the treatment of Severe Acute Respiratory Syndrome-Coronavirus-2","authors":"William Zhang, A. Daher, A. Gatignol, Robert J. Scarborough","doi":"10.26443/msurj.v16i1.62","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.62","url":null,"abstract":"SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. As the 2019 coronavirus disease continues to spread, it will be useful to have as many effective treatment options as possible. This research has the potential to create a siRNA treatment that is safe, effective, and practical in design and administration; 192 siRNAs were designed to target conserved regions of the SARS-CoV-2 genome. The first aim of this study is to confirm, via sequence analysis, that these target sites have remained highly conserved over the course of the pandemic. Multiple sequence alignments were generated for the first half of 30,312 full SARS-CoV-2 genomes, which were averaged and compared with the Wuhan-Hu-1 reference genome. Most target sites maintained a very high level of conservation, suggesting that potential repressor siRNAs could be effective in a majority of infected individuals. To evaluate the efficacy of the 192 test siRNAs, we cloned sections of the SARS-CoV-2 RNA genome into GFP fusion genes. Some of these constructs were transfected in different conditions to set up a screening assay based on GFP expression. Preliminary data on the setup of this GFP reporter assay show that the M, N, E, ORF8, and ORF10 constructs produced a good GFP signal, whereas the S, F1, F2 and F3 constructs did not produce a sufficiently strong GFP signal to detect above background. In a preliminary experiment, we evaluated siRNAs targeting the M, N, and E open reading frames and found some to be efficacious. Future directions for this project include generating alignments of the second half of the SARS-CoV-2 genome for a complete sequence conservation estimate, and cell metabolism assays for supplementing visual observations of siRNA toxicity, optimization of GFP readout, and screening of all designed siRNAs.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42674234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Convective Rolls in a Compressible Fluid 可压缩流体中的对流滚动

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.60

Katherine J. Simzer, G. Lewis

{"title":"Convective Rolls in a Compressible Fluid","authors":"Katherine J. Simzer, G. Lewis","doi":"10.26443/msurj.v16i1.60","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.60","url":null,"abstract":"Rayleigh-Bénard convection occurs between two horizontally infinite plates when the lower plate is heated with respect to the upper one. The temperature gradient between the two plates causes convective rolls to form as the warmer fluid below becomes more buoyant than the cooler fluid above it. The standard (classical) analysis uses the Boussinesq approximation, which neglects the variations of fluid density except in relation to buoyancy forces. This approximation is not accurate for some real-world applications. This project is inspired by the atmosphere, so we will consider the onset of convection in a vertically stratified layer of fluid which we model using the anelastic equations. The standard analysis is presented in many textbooks and is used as a comparison to the analysis for the compressible fluid presented here. Using linear stability analysis, we compute the critical temperature differences required to induce convection. It is not possible to find analytical solutions, and therefore, numerical methods implemented in Python using LAPACK subroutines are used. Results of the critical Rayleigh number at the half-height of the fluid for a range of plate separation distances are computed. For all the cases that are considered, the solution for the compressible problem follows the standard solution for plate separation distances smaller than some viscosity-dependent value that increases with the viscosity of the fluid. For larger d, it is observed that the stratification inhibits the onset of convection. Our solution is far more idealized than any actual convection happening in the atmosphere. However, it does demonstrate, in this context, the limits of the Boussinesq approximation.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44640279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Eco-Audit of MOFs as H₂ Storage Materials for Vehicle Applications, Using Novel Refueling Model MOFs作为H的生态审计₂ 使用新型换料模型的车辆应用存储材料

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.54

Elias Andraos, Guido Merino, Maximilian Ritter

{"title":"Eco-Audit of MOFs as H₂ Storage Materials for Vehicle Applications, Using Novel Refueling Model","authors":"Elias Andraos, Guido Merino, Maximilian Ritter","doi":"10.26443/msurj.v16i1.54","DOIUrl":"https://doi.org/10.26443/msurj.v16i1.54","url":null,"abstract":"Metal-organic frameworks (MOFs) are a heavily researched candidate for fuel-cell electric vehicle (FCEV) hydrogen storage. However, little analysis has been done on the environmental impact of potential MOF vehicles compared to established alternative vehicles, such as compressed hydrogen or battery-electric vehicles. In this work, a preliminary eco-audit was conducted for a FCEV using an MOF hydrogen storage system based the best current MOF Ni₂(m-dobdc) (Ni-MOF-74). (1) Cost and environmental impact analyses were performed for both the production and use phases of an MOF-FCEV. The cost and environmental impact of MOF production was compared to that of Lithium Nickel Manganese Cobalt Oxide (LiNMCO) batteries, the current state-of-the-art for BEVs. (2) Environmental impact was assessed using embodied energy estimates based on reported values for LiNMCO BEVs. These highlighted MOF vehicles as a competitor to current renewable energy vehicle technologies. For the use phase, a hydrogen refueling station that produces hydrogen onsite by proton exchange membrane (PEM) electrolysis from grid electricity was compared to an equivalent population of battery electric vehicles (BEVs) charged at distributed recharging stations. FCEVs using the proposed refueling model were able to compete with BEVs both in terms of electricity CO₂ footprint and cost in the simulated solar-dominated Californian grid, but not in the hydro- and nuclear-heavy Ontario grid.","PeriodicalId":91927,"journal":{"name":"McGill Science undergraduate research journal : MSURJ","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46720038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Changing Climate Change 不断变化的气候变化

McGill Science undergraduate research journal : MSURJ Pub Date : 2021-04-15 DOI: 10.26443/msurj.v16i1.66

Maya Willard-Stepan, A. Fong, Yehia Sabaa

引用次数: 2