Synthetic Biology Club

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  • Time and duration: Last Mondays of every month at 12h00 (EST) over 1 hour; 30-40 minutes for oral presentation and 10 minutes for questions.
  • Meetings are held in English.
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For any issues or questions, please contact the organizer of this event:
Mr. Benjamin Ouellet.

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Note: Rows highlighted in “Light Red" are of future meetings.
Note: Recordings of previous meetings are also available on the AMSBL’s YouTube Channel (for speakers who authorized the publication of their talks).

Date (M/D/Y) Presenter and Topic
Teresa Garcia-Ybarra PhD student Research Project 10/25/2021 Engineering of selenoneine in microbial hosts using synthetic biology return false; Selenoneine, is an organic selenium compound, commonly found in the blood and tissues of several marine species. This molecule shows antioxidant activity against reactive oxygen species (ROS) and can neutralize mercury toxicity and is thus known for its health protective effects in many human diseases. Nonetheless, no economically viable means for selenoneine production has yet been established.
The aim of this project is to develop synthetic biology strategies to engineer selenoneine-overproducing microbial hosts to allow its subsequent purification and characterization. To achieve this, design-build-test cycles for metabolic engineering will be iteratively repeated until desired selenoneine titers are produced, and the health protective effects of engineered strains will be investigated in zebra fish.
This project will result in the development of engineered strains that might support a cheap, renewable, and scalable production of selenoneine. Laval University – Faculty of Science and EngineeringDepartment of Biochemistry, Microbiology and BioinformaticsInstitute of Integrative and Systems Biology (IBIS)Quebec (Quebec), Canada Teresa García Ybarra received a bachelor’s degree in Agroindustrial Engineering at Chapingo Autonomous University a recognized agricultural university in Mexico and Latin America. Then completed a master’s degree in Synthetic Biology and Biotechnology at the University of Edinburgh in the UK. Her master’s degree dissertation was supervised by Prof. Christopher French (School of Biological Sciences) and involved the application of synthetic biology approaches to engineer Escherichia coli for second generation biofuel production. She recently started her PhD in biochemistry under the supervision of Prof. Ahmad Saleh, her project aims to develop synthetic biology strategies to engineer selenoneine-overproducing microbial hosts to allow its subsequent purification and characterization and to study selenoneine health protective effects. She is interested in synthetic biology, synthetic chemistry, metabolic engineering and biotechnology, and it’s use to produce novel and industrially relevant compounds.
Benjamin Ouellet MSc student Research Project 11/29/2021 Impact of modulating Cas9 expression on the efficiency of CRISPR-Cas9-mediated genome editing in Yarrowia lipolytica return false; CRISPR-Cas is a powerful tool for genome editing. This tool demonstrated a great success in the genetic manipulation of Yarrowia lipolytica that opened the doors towards harness the lipogenic potential of this yeast towards the production of essential polyunsaturated fatty acids, biodiesel and other oleochemicals. To enhance protein expression, a synthetic hybrid promoter consisting of eight upstream-activating sequences in tandem fused to the TEF promoter was previously proposed and is currently used for the expression of Cas9 in CRISPR-Cas9-mediated genome editing protocols for Y. lipolytica. However, tandem repeats are difficult to manipulate or clone. Here we report a truncated version of the native TEF promoter of Y. lipolytica. Our results showed that this truncated TEF is a significantly stronger promoter than UAS1B8-TEF as estimated using GFP reporter genes. Comparison of genome editing using Cas9 under the two promoters revealed that the truncated TEF leads to higher gene deletion efficiency. We propose this new truncated TEF promoter to drive Cas9 expression to enhance its expression and hence its genome editing efficiency. Moreover, being shorter, truncated TEF is also easier to manipulate. Laval University, Faculty of sciences and engineering, Department of biochemistry, microbiology and bioinformatics, Quebec, Canada. - Laval University, Institute of Integrative and Systems Biology, Quebec, Canada Benjamin Ouellet graduated with a bachelor degree of Biochemistry from Laval University. During his bachelor's degree, he joined the iGEM team of Laval University to compete in the international synthetic biology’s competition of iGEM where he worked on a project he initiated. Motivated by his interest in synthetic biology and applied sciences, he joined the team of the Abdel-Mawgoud Synthetic Biology Lab where he is currently conducting his master’s degree under the supervision of Ahmad Saleh, PhD. His project aims to develop a new platform for the biosynthesis of biodiesel using Yarrowia lipolytica with the purpose of producing more efficient and ecofriendly biofuels.
Bruno Arcand MSc student Research Project 1/31/2022 Development of tools for genetic engineering of bacterial cellulose production in Komagataeibacter return false; Cellulose harvested from plants is the most common polymer of biological origin, and we already use it extensively as it is an important component of wood, cotton, paper, and other materials. However, bacterial cellulose, or BC, exhibits unique properties that make it especially suited for a plethora of applications, such as water filtration, high-quality bandages, and optoelectronics. BC is produced at the air/medium interface of liquid cultures of some bacteria, including the Komagataeibacter genus, and are easily harvested and processed.However, production of BC at an industrial scale meets important challenges, such as low yields and instability of cellulose production in culture, which translate to high production costs. Moreover, there is a lack of molecular biology tools adapted for use in BC-producing bacteria. This project aims to build a toolkit for the genetic engineering of BC-producing bacteria and use it to produce an optimized strain for industrial-scale BC production by addressing these challenges directly at their source.So far, we identified a suitable plasmid backbone, multiple selection markers and their resistance cassettes, and built a synthetic CRISPR-Cas9 gene codon-optimized for use in Komagataeibacter. Additionally, we produced a library of BC-nonproducing mutants of Komagataeibacter rhaeticus iGEM, and deciphered one of the mechanisms responsible for the inactivation of the genes responsible for BC production. - Laval University, Faculty of sciences and engineering, Department of biochemistry, microbiology and bioinformatics, Quebec, Canada. - Laval University, Institute of Integrative and Systems Biology, Quebec, Canada Bruno Arcand first graduated with a Bachelor's degree in Microbiology from Sherbrooke University. He already demonstrated a keen interest in genetic transformation techniques such as CRISPR-Cas9 and their many applications, but it is during the internships he did as part of his Bachelor’s degree that he caught the Synthetic Biology bug. He then joined the team of the Abdel-Mawgoud Synthetic Biology Lab where he is conducting a Masters' degree in Microbiology under the supervision of Pr. Ahmad Saleh and Pr. Younès Messaddeq. His project aims to produce a toolkit for genetic engineering of cellulose-producing bacteria, and use them to successfully engineer a cellulose-overproducing strain.
Meryam Magri PhD student Published Article 2/28/2022 Identification of putative producers of rhamnolipids/glycolipids and their transporters using genome mining Rhamnolipids (RLs) are microbial glycolipids (GLs) with interesting structure dependent bioactivities and physicochemical properties qualifying them for diverse medical and industrial applications. Discovery of RLs with more interesting bioactivities and properties relied on laborious screening of new RL producers isolated from the environment, which resulted in the redundant identification of already known RL producers and structures. Here, we present a genome mining approach that resulted in the identification of 80 RLproducing species (including the two reference species), 71 of which were never reported before. Distance trees of their RL biosynthetic enzymes, RhlAB, allowed the identification of 11 distinct clades. Preliminary experimental validation using thin layer chromatography on one non-pathogenic RL-/GL-producer, Nevskia soli , confirmed its putative production of RLs. Additionally, this study led to the discovery of the putative RL transport mechanism involving 3 transmembrane proteins whose coding genes are highly conserved and are mostly clustered with one of the RL biosynthetic gene clusters in most RL-/GL-producers identified in this study Medical Biotechnology Laboratory (MedBiotech), Faculty of Medicine and Pharmacy, Mohammed 5 University of Rabat Meryam Magri is currently a PhD student in the Faculty of Medicine and Pharmacy of the Mohammed 5 University of Rabat, Morocco, she had a bachelor’s degree in Computer science at the Cadi Ayyad University of Marrakech, Morocco and she had completed a master’s degree in bioinformatics at the Faculty of Medicine and Pharmacy of the Mohammed 5 University of Rabat, Morocco. Her master’s degree dissertation was supervised by Pr. Abdel-Mawgoud where she worked on the identification of putative producers of rhamnolipids/glycolipids and their transporters using diffrent genome mining approaches
Patrick Diep PhD student Other 3/28/2022 Dissolving disciplinary siloes in synthetic biology undergraduate curriculum development return false; Synthetic biology (herein synbio) is interdisciplinary in nature. The flavours of synbio that many of us are most familiar with are the experimental, mathematical, and computational spices, but there are more spices on this rack: social sciences, intellectual property, governance, entrepreneurship and more. To cook up a synbio project based on strong fundamental principles, guided by problems that exists in society and the environment, a team of synbio practitioners is required to increase a synbio innovation’s technology readiness level. Whether these teams be in the iGEM competition, industrial R&D, academic labs focusing on translational research, start-ups etc., we have one question at CSBERG: are we training students to have a career in such dynamic settings? In this presentation, we explore this question by first discussing the state of synthetic biology education from the perspective of iGEM students in 2019 and use these insights to ground our curriculum development for an introductory synbio course for the general undergraduate audience. Two iterations’ worth of quantitative/ qualitative data for SYNB1 – Fundamentals of Synthetic Biology and SYNB2 – Synthetic Biology Implementation Sciences will be presented, and how these findings are deployed in our third course offering this summer: SYNB3 – Introduction to Integrative Synthetic Biology is elaborated on. Future research directions are presented along with opportunities to volunteer with CSBERG in the future. Canadian Synthetic Biology Education Research Group, CSBERG - University of Toronto, Department of Chemical Engineering and Applied Chemistry, BioZone Centre for Bioengineering and Applies Bioscience Patrick is a senior PhD candidate at the University of Toronto’s BioZone Centre for Bioengineering and Applied Bioscience with prior training in biochemistry and synthetic biology at the University of Waterloo. He studies how metalloproteins interact with metal ion species in complex solutions for the purpose of protein-based nickel recovery from mine effluents. He is also the co-founder of Lyrata, a start-up that 3D-prints re-usable soil for hydroponic farming operations that has received $200K in pre-seed funds; and program director/ founder of CSBERG, the Canadian Synthetic Biology Education Research Group.
Vivek Morya Professor Published Article 4/25/2022 Homology modeling and virtual screening of P-protein in a quest for novel antimelanogenic agents A piece of adequate knowledge on the molecular mechanism of melanogenesis provides an opportunity to find novel molecular targets for the discovery and development of new cosmetics. Among various genes, the OCA2 is being essential for proper melanin synthesis, and mutation or deletion of this gene leads to oculocutaneous albinism type 2. Thus, for this study, the product of this gene, that is P-protein, was targeted in the quest for novel inhibitors as antimelanogenic agents. Based on a pattern search of amino acid sequence and homology analysis, the protein structure was modelled. The role of this protein has been predicted as a tyrosine transporter of melanosomes. Thus, the molecular library was generated on the basis of tyrosine transporter inhibitor. Based on the dock score, 20 molecules have been considered as putative inhibitors for P-protein. Among these compounds, five molecules (compound #1, #4, #8, #13 and #17) were found to be quite effective as antimelanogenic without having any toxicity. Further investigations to establish the mechanism of action, the indirect methods such as tyrosinase assay, analysis for eumelanin and pheomelanin and investigation of mRNA levels were being carried out. The results from the studies offered a new lead in antimelanogenic therapy and may be very useful for further optimization work in developing them as novel depigmenting agents. Department of Orthopedic Surgery, Kangnam Sacred Heart Hospital, Hallym University, School of Medicine, Seoul, Republic of Korea Dr Vivek Morya is an Industrial biotechnologist, he worked at several universities and institutions of international repute. Currently, he is Chief Scientist at the Centre for Energy and Environmental sustainability, India; CTO, Agriculture and Forest Conservation Research Centre, Nepal; Team Leader, Kangnam Sacred Heart Hospital, Hallym University, Seoul, South Korea. He has worked, as an assistant professor, at Inha University, South Korea, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India. He worked as Chief Scientist at SS MASER Technology Private Limited, India, Scientist at DST-CPR Govt of India; as a Researcher at CSIR-NBRI, CSIR-NIIST, DDU Gorakhpur University, India. Dr Morya has published more than 45 research articles, 12 patents, 5 book chapters, 28 microbial accessions, and 2 edited books (Under process). Dr Morya is also serving as an editorial board member of various journals of international repute.
Franziska Hemmerling Postdoctoral fellow/associate Published Article 5/30/2022 Strategies to access biosynthetic novelty in bacterial genomes for drug discovery Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and ‘biosynthetic dark matter’, revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty. ETH Zurich, Institute of Microbiology, Zurich, Switzerland Since 2017, Franziska is a postdoctoral researcher with Prof. Jörn Piel at the Institute of Microbiology at ETH Zurich, Switzerland. She is driven by her interest in drug discovery and harnessing biosynthetic enzymes for synthetic biology. Her main research topics are the investigation of new biochemistry in trans-AT PKS biosynthetic pathways as well as linking bacterial biosynthetic gene clusters to their respective encoded marine natural products.
Haitham Elmarakeby Instructor Published Article 6/27/2022 Interpretable Machine Learning for Discovery in Cancer Despite advances in prostate cancer treatment, including androgen deprivation therapy, metastatic castration-resistant prostate cancer (mCRPC) remains largely incurable. Recent advances in collecting and sharing large quantities of genomic records from patients with primary and metastatic prostate cancer have not yet been matched with advances in computational model development to shed light on the underlying biology of mCRPC. Here we developed a biologically informed deep learning model (P-NET) that can accurately identify advanced prostate cancer samples based on their genomic profiles. By using a sparse model architecture that encodes different biological entities including genes, pathways, and biological processes, we were able to interpret the model in a way that is not matched by typical deep learning models. In a systematic unbiased way, P-NET recovered known biology of mCRPC via AR, TP53, RB1, and PTEN disruption, as well as less expected genes such as MDM4. We showed experimentally that MDM4 mediates enzalutamide resistance, showing that it may be a potential therapeutic target. We envision that our model will be helpful in both predicting clinical outcomes of cancer patients and generating biological hypotheses to better understand the underlying cancer biology. Dana-Farber Cancer Institute | Harvard Medical School | Broad Institute of MIT and Harvard Haitham Elmarakeby is an instructor at Dana Farber Cancer Institute and Harvard Medical School. He is also an affiliate researcher at the Broad Institute of MIT and Harvard. ​​His research is focused on using machine learning to better understand cancer progression and therapeutic resistance in cancer patients. Elmarakeby’s current research focuses on building interpretable models to discover novel markers of clinical and biological outcomes in multiple cancer types including prostate, breast, lung, and melanoma cancers. Elmarakeby earned a BSc from the Systems and Computer Department at Al-Azhar University in Cairo, Egypt, and his MSc from the Computer Engineering Department at Cairo University. He completed his Ph.D. in Computer Science at Virginia Tech and got his postdoctoral training at the Dana-Farber Cancer Institute.
Muyiwa Adegbaju PhD student Research Project 7/25/2022 Analysis of interactions between glucan, water dikinase and starch branching enzymes in determination of starch structure return false; Starch is one of the most bountiful polymers synthesized in nature and is produced as a storage carbohydrate throughout the plant kingdom. It's the most vital component of storage organs in many plants and is a functional polymer with the capacity for providing ecological friendly bio-materials. Starch physical properties and usefulness depend upon many factors, including the proportion of its two polyglucan components (amylose and amylopectin) and the degree of phosphate substitution. Since native starch usually require artificial modification, manipulating starch metabolism to produce plants which accumulate starch with improved properties for industry has long been a goal of plant biotechnologists. Although much knowledge has been produced about the enzymes involved in starch biosynthesis, less is known about how they functionally interact with each other. Such knowledge is essential to help the rational design of starch biosynthesis for production of this environmentally friendly industrial feedstock. In this project, transgenic potato plants that are simultaneously repressed in genes whose products are glucan, water dikinase (GWD) and starch branching enzymes (SBEs) were manufactured through RNAi technology. Increase in apparent amylose content was observed in the starch extracted from tubers of the transgenic lines and consequent upon the alterations in starch composition, the granule morphology, swelling power and freeze-thaw stability of the starch were also altered. Institute of Plant Biotechnology, Stellenbosch University, South AfricaDepartment of Crop Production, The Federal University of Technology Akure, Nigeria Adegbaju Muyiwa Seyi is a doctoral candidate under the supervision of Prof. J. R. Lloyd at the Institute of Plant Biotechnology in Stellenbosch University (SU) and supported by NRF-TWAS African renaissance doctoral scholarship for research in South Africa. His doctoral research (now awaiting final oral presentation) is aimed at elucidating functional interaction between some starch metabolic enzymes in Solanum tuberosum L. He was awarded M. Agric. Tech. in 2015 and B. Agric. Tech. in 2010 all in the department of Crop, Soil and Pest Management at the Federal University of Technology Akure (FUTA) Nigeria, where he also worked as teaching assistant from April 2014 to December 2015. In January 2016, he accepted the position of assistant lecturer at the department where he obtained his first and second degree and taught courses on genetics and biotechnology prior to commencement of his study at SU in March 2018. He's currently an enthusiast in bio-economy and thoroughly enjoy research in this area.
Zacharie Morneau MSc student Research Project 10/31/2022 Medium optimization for high lipid production by Yarrowia lipolytica and Rhodotorula toruloides using an optimized Nile Red-based lipid fluorometry As lipogenic yeasts are becoming increasingly harnessed as biofactories of oleochemicals, the availability of efficient protocols for the determination and optimization of lipid titers in these organisms is necessary. In this study, we optimized a quick, reliable and high throughput Nile Red-based lipid fluorometry protocol adapted for oleaginous yeasts and validated it using different approaches, the most important of which is using Gas chromatography coupled to flame ionization detection (GC-FID). This protocol was applied for the optimization the concentrations of ammonium chloride and glycerol for the highest lipid titers in Rhodotorula toruloides NRRL Y-6987 and Yarrowia lipolytica W29 using response surface central composite design (CCD). The optimal concentration of ammonium chloride and glycerol are 8,8 and 125 g/L, respectively, that achieved a C/N ratio ~25 above which lipid production decreases rapidly. The developed regression models and response surface plots give an insight on the careful selection of optimal C/N ratio for maximal lipid production Department of biochemistry, microbiology and bioinformatics, Laval University, Canada | Institute of Integrative and Systems Biology, Laval University, Canada I am currently a Biochemistry Master's student in Sylvain Moineau's laboratory. My current work focuses on investigating phage protein interactions with their hosts using different techniques including genome engineering. During my bachelor's degree, I did two summer internships, one of which was with Prof. Ahmad Saleh. During this internship, I worked on the project I am presenting today, which focuses on a new method of lipid titer measurement using fluorescent dye Nile red. This project, which we are concluding, ended in the redaction of an article where we used the method to optimize medium composition for lipid accumulation in R. toruloides and Y. lipolytica using central composite design.
Sebastien Rodrigue Professor Research Project 11/28/2022 Engineering bacterial conjugation for microbiome editing Antibiotic resistance threatens our ability to treat infectious diseases, spurring interest in alternative antimicrobial technologies. The use of bacterial conjugation to deliver CRISPR‐Cas systems programmed to precisely eliminate antibiotic‐resistant bacteria represents a promising approach but requires high in situ DNA transfer rates. We have optimized the transfer efficiency of conjugative plasmid TP114 using accelerated laboratory evolution. We hence generated a potent conjugative delivery vehicle for CRISPR‐Cas9 that can eliminate > 99.9% of targeted antibiotic‐resistant Escherichia coli in the mouse gut microbiota using a single dose. We then applied this system to a Citrobacter rodentium infection model, achieving full clearance within four consecutive days of treatment. Our results suggest that engineered probiotics could provide an interesting alternative to antibiotics in the prevention or treatment of infections and dysbiosis. Department of Biology, Sherbrooke University, Quebec, Canada Sébastien Rodrigue completed a Ph.D. in Biology at the Université de Sherbrooke and postdoctoral studies at the Massachusetts Institute of Technology (MIT) where he developed new methods for single-cell genome sequencing. He has also developed various approaches that have become common for metagenomic studies and in integrative projects combining several types of omics data. In 2010, he was recruited to the Département de biologie at the Université de Sherbrooke where his research projects focus on genomics, systems biology, and synthetic biology. His group uses innovative techniques for cloning and transplanting complete bacterial genomes using the near-minimal organism Mesoplasma florum as a model. He is also interested in highly-engineered Escherichia coli strains and in the engineering of probiotics as live biotherapeutic strains capable of modifying microbial populations of the intestinal microbiota. Dr. Rodrigue is also a co-founder and CSO of TATUM biosciences, a biotech company developing advanced biologics for oncology produced by programmable bacteria.
Saleem Iqbal Postdoctoral fellow/associate, Research scientist Other 1/30/2023 Drug Discovery therapeutics as evidenced through Systems Pharmacology Background: System medicine approaches have played a pivotal role in identifying novel disease networks especially in miRNA research. It is no wonder that miRNAs are implicated in multiple clinical conditions, allowing us to establish the hubs and nodes for network models of Alzheimer's Disease (AD). δ-secretase, also known as asparagine endopeptidase (AEP) or legumain (LGMN), is a lysosomal cysteine protease that cleaves peptide bonds C-terminally to asparagine residues in both amyloid precursor protein (APP) and tau, mediating the amyloid-β and tau pathology in AD. Methods: Protein-Protein Interaction (PPI) networks of LGMN or δ-secretase were constructed using the Genemania database. Network Analyzer, a Cytoscape plugin, analyzed the network topological properties of LGMN. miRNAs related to Alzheimer's were extracted from the HMDD (Human microRNA Disease Database) and experimentally verified miRNA-gene interaction was obtained by searching miRWalk. Starbase v2.0 and miRanda were used for screening miRNA of LGMN genes. Conclusion: In a first-of-its-kind study, the LGMN gene-related regulatory miRNAs resulted in the identification of AD-specific TFs and miRNAs involved in AD. Our findings reveal the dysregulated miRNA: hsa-mir-26b-5p could be used as a biomarker in the diagnosis of AD. Moreover our 200ns molecular dynamic simulations revealed oprea1 as identified drug and its stablity into the binding pocket of the δ-secretase. CHU Research Center and Department of Molecular Medicine, Laval University, Quebec, Canada. Dr. Saleem Iqbal is an award recipient for Structural Virology-SARS-CoV-2 project, currently working as Senior Postdoctoral fellow at Dept. of Molecular medicine Chu de Quebec hospital, Canada. His current work focusses on SARS-CoV-2 drug discovery therapeutics. As a Neuroscientist, Biophysicist, Crystallographer and structural bioinformatician, he uses his expertise in protein folding, System Biology, Molecular modelling, Ligand design, SAR, Molecular dynamics simulations to understand and study important human diseases such as Alzheimer’s Disease, Parkinson’s disease, COVID-19 therapeutics and Cancer at different interfaces. He has been Visiting Professor at the School of Pharmaceutical Education and Research at Jamia Hamdard University and School of Biotechnology at Bennett University. He earned his Ph.D., in Bioinformatics-Crystallography and Biophysics-Interdisciplinary from prestigious Biophysics Department, University of Madras- which is home of pioneering discoveries viz., Triple Helical Structure of Collagen, the famous Ramachandran plot for the protein structure and application of anomalous scattering methods. He worked as Research Associate for Prostate Cancer therapeutics at Bioinformatics Lab funded by Department of Biotechnology, India. He also worked as Senior Research Associate at Prestigious Department of Computational and Data Sciences (CDS), Indian Institute of Science, Bangalore., where his publication on secretase biology "Discovery of microRNAs as biomarkers targeting the delta secretases" is a key finding in Alzheimer’s Disease. He is recipient of various travel awards. Dr. Saleem Iqbal major projects have been funded by Alzheimer’s Association, EMBL and CIHR.