A research article first published in February 2023 on the characterization of diverse DNA aptamers for recognition of COVID-19 has been featured on the cover of the most recent issue (issue #5) of the journal Analysis & Sensing.
We’re all very excited and overjoyed with the recognition of all the hard work that’s being done here in the lab.
For the full article, check out the following link:
For more papers, see the Publications page of the website.
Shuwen successfully defended her thesis a couple of weeks ago which means that she is close to receiving her actual piece of paper certifying she has completed her PhD!
Some thoughts of Shuwen on her PhD journey:
Doing a PhD IS challenging, even beyond what I had imagined five years ago when I started this journey. This road trip, which I expected to have ups and downs and go back and forth, sure was a rollercoaster. If I am honest, most of the time (for me) was more of a down and back experience. However, I was fortunate enough to find my way out of those downs and back into some ups with incredible help and support of my supervisors, other lab members, and peers. It has been such a long way that it felt quite surreal that I made it to the point where I got to defend my PhD thesis, and it didn’t even feel real yet when we were all gathered at the Phoenix for my defence celebration. I feel truly blessed for this achievement and am beyond proud of myself. I chose to stay strong, to stick through it and make things happen. There’s definitely a weight off my shoulders now and I’m feeling so free, which I wish to be in the rest of my life also: To be free, always.
It’s true that a PhD isn’t an easy journey, but it’s supposed to shape you into a better scientist. We are all incredibly proud of the scientist Shuwen has become throughout the years and we look forward to see what’s next for her!
The Biochemistry & Biomedical Sciences Summer Scholars Program (SSP) is a 12 week immersive research and mentorship program awarded to 9 undergraduate scholars this year for the second time since its establishment. I have had the pleasure of joining The Li lab through the SSP in May of 2023. Under the direct mentorship of Dr. Li & Jim Gu, my project focused on investigating DNAzyme activity in the cleavage of a specific RNA modification.
This experience not only allowed me to understand and support ongoing research efforts, yet also see first hand the true humanity behind all the research done in The Li lab and McMaster’s Biochemistry & Biomedical Sciences Department. As an undergraduate student now entering my second year in the Honours Biochemistry program here at McMaster, the ability to connect with other like minded undergraduate students, graduate students, post doctoral fellows, faculty members and research staff, is truly unparalleled to anything I have experienced before.
I am continuously grateful for this opportunity and the chance to connect with so many talented, kind, as well as genuine people this past summer.
~ Tegvir S. Grewal
In July, I brought students and staff of my laboratory to Blue Mountain for a lab retreat. We had 22 people join in the fun, but unfortunately 7 couldn’t make it. We spent the days making breakfast and lunch ourselves, and we visited local restaurants two evenings for dinner. The final night was Taco Night, and we prepared dinner ourselves. Arguably the best dinner of all the days.
We played games, sang songs, and did various sports activities including volleyball, tennis, basketball, golf, running, hiking, and beach volleyball. The days of the retreat were filled with joy, relaxation, singing, and friendship, and I have fully appreciated the hobbies and talents of the students outside of science. It turns out that my lab has amazing athletes, singers, organizers, cooks, storytellers, and comedians.
They can work hard and play hard, and are just an amazing group of lovely young people. Even though everyone comes from all over the world with different backgrounds, everyone has a kind and beautiful heart and a willingness to help others.
I couldn’t be more honoured and proud to have such a very happy, kind, and helpful laboratory family. This trip not only allowed me to get to know them better, but it also allowed everyone to strengthen their friendships.
Money and time well spent for a priceless memory that we’ll all carry with us. Couldn’t be happier with the current team and dynamics that we have going in our lab!
– Dr. Yingfu Li
Learn about the lab’s recent work on the detection of Salmonella for food safety here https://brighterworld.mcmaster.ca/articles/salmonella-solution-researchers-develop-rapid-test-for-food-contamination/
Angewandte Chemie International Edition has a Press Release for this work:
https://onlinelibrary.wiley.com/page/journal/15213773/homepage/press/202315press.html.
CTV news report our story, “McMaster researchers develop salmonella solution”
https://www.ctvnews.ca/video?clipId=2669669.
Jiuxing Li, Shadman Khan, Jimmy Gu, Carlos D. M. Filipe*, Tohid F. Didar*, Yingfu Li*. A simple Au-on-Au colorimetric sensor for food-borne pathogen Salmonella typhimurium. Angew. Chem. Int. Ed. 2023, e202300828. (DOI: 10.1002/anie.202300828, IF: 16.8)
Congratulations to Jiuxing for his work as a guide editor and advisor for several journals.
He has served as a guest editor for Sensors and Frontiers in Chemistry, Sensors for special issue “Micro/Nano Biosensors and Devices”, Frontiers in Chemistry for Research Topic “Advanced Nanomaterials for in Vitro Diagnostics” and as a topical advisory panel member of sensors.
In this review, we are proud to share the incredible work done globally in developing aptamers for the COVID-19 pandemic. Given their desirable characteristics as molecular recognition elements, nucleic acid aptamers were of significant interest to multiple labs worldwide over the past few years. Our review paper features a comprehensive comparison between the most notable SARS-CoV-2 aptamers, taking a detailed look at the SELEX strategies, sequence alignments, secondary structures, and multimeric engineering achievements. We also highlight the application of these aptamers as ligands for therapeutic agents and biosensor development. Overall, aptamers represent a compelling solution to the diagnostic and therapeutic challenges of COVID-19, and we hope this review propels further aptamer research for current and future pandemics.
Read more about the paper here: https://doi.org/10.1002/anse.202200012
-Ryan
We are excited to announce our recent review paper on the use of nucleic acids in electrochemical biosensors in collaboration with the Dr. Soleymani lab. Nucleic acids have unique structural motifs that allow them to bind non-nucleic acid targets (aptamers) and catalyze chemical reactions (DNAzymes), making them excellent candidates for use in biosensors. This review paper highlights the historical evolution of nucleic acids as probes in electrochemical biosensors and provides specific examples of their use in clinical settings such as infectious disease, cancer, and cardiovascular health. DNA, in particular, has proven to be an ideal biorecognition element and redox reporter probe due to its ability to be easily modified with various functional groups. We hope that our review will serve as a valuable resource for researchers in the field of biosensors and contribute to the development of new diagnostic tools for a wide range of diseases. Read more about it here: https://doi.org/10.1002/anie.202212496
-Zijie
Read about our recent work on applying the 10-23 DNAzymes for RNA detection. https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202300075
Read our latest work on SARS-CoV-2 detection in saliva, where we developed a trimeric aptamer, named TMSA52, for the recognition of SARS-CoV-2 spike protein. The aptamer not only possesses superb binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity. Using Pd-Ir nanocubes as nanozymes in an enzyme-linked aptamer binding assay (ELABA), TMSA52 was capable of sensitively detecting diverse pseudotyped lentiviruses in pooled human saliva. The ELABA was also used to test 50 SARS-CoV-2 positive and 60 negative patient saliva samples, providing sensitivity and specificity values of 84.0% and 98.3%, respectively, thus highlighting the potential of TMSA52 for the development of future rapid tests.
Read our recent review on the discovery and translation of functional nucleic acids developed in our lab.
The Li Lab in collaboration with the Soleymani and Hoare labs have published our work to develop a rapid test for Porcine Epidemic Diarrhea Virus. Read more about it here https://onlinelibrary.wiley.com/doi/10.1002/anie.202204252
We’re excited to share our latest work on SARS-CoV-2 where we expand on our previous publications and describe an aptamer class that binds all major variants of concern with high affinity. This is an important tool for the development of aptamer based COVID detection technologies that can be specific, sensitive and robust for the detection of current and possibly future variants. Read more about our work here. -Jim
Aptamers are nucleic acids that are capable of recognizing target molecules. Over the past 30 years, thousands of aptamers have been discovered by scientists via in vitro selection technique. This review examined the range of targets as well as the affinity and specificity of ~1000 generated aptamers. By comparing the synthetic aptamers with natural riboswitches, protein-based recognition elements, a gap between synthetic aptamers and natural recognition elements was revealed. A series of ideas for developing better aptamers were proposed to solve the real world problems. We hope these strategies can help aptamers remain high functionality in application environment. Happy reading 😊 – Shuwen Qian
Qian, S.; Chang, D.; He, S.; Li, Y. Aptamers from Random Sequence Space: Accomplishments, Gaps and Future Considerations. Analytica Chimica Acta 2022, 1196, 339511. https://doi.org/10.1016/j.aca.2022.339511
Letizia will be joining the lab as a Ph.D. student. She will be working on stool biosensor technologies for applications in ecological protection.
Following up on our recent report of high-affinity DNA aptamers for SARS-CoV-2, we’ve been busy working with our collaborators in the Soleymani Lab and the Biointerfaces Institute to apply them on electrochemical sensors. Read our latest COVID19 paper at Pubmed to learn more about how we achieve high sensitivity detection of SARS-CoV-2 in unprocessed human saliva to pave the way for a rapid and sample diagnostic test.
Take a quick look at our recent publication in Frontiers in Chemistry. In this paper, a simple and surfactant-free approach is presented to synthesize Pd-Ir nanocubes with atomic Ir shell thickness in an aqueous solution at room temperature. Biomolecules such as antibodies and nucleic acids have free access to the surface of Pd-Ir nanocubes. Applications of Pd-Ir nanocubes in immunoassays and aptamer-based biosensors are realized, exploiting the excellent peroxidase activity and fluorescence quenching ability of Pd-Ir nanocubes. Read more about our work at Pubmed. – Jiuxing
Li J, Li Y. Facile Synthesis of Pd-Ir Nanocubes for Biosensing. Front Chem. 2021 Nov 24;9:775220. doi: 10.3389/fchem.2021.775220. PMID: 34900937; PMCID: PMC8651546.
Finally had the opportunity to get everyone together for a group lunch, great to see everyone in person again.
The Li Lab welcome our newest member, Giulia Core, who will be joining us as a visiting Ph.D. student from the University of Glasgow. She will be working on molecular diagnostic technologies.
The Li Lab and our collaborators from across the McMaster community have published our first report on our novel aptamers for COVID19! The lab has refocused our efforts over the past year to address pressing COVID19 problems and we’re excited to finally be sharing our work. Read more about our work at Pubmed.
In a collaboration with the Didar Lab and Toyota Tsusho Canada, the Li Lab will be working towards the development of food wrap technologies for the detection of pathogenic bacteria using DNA sensors. Read more about it McMaster Brighter World.
Li Lab postdoctoral fellow Erin McConnell has been awarded the NSERC & L’Oréal-UNESCO Women in Science Supplement. Congratulations to Erin for her fantastic work as a scientist and as a role model for young scientists around the world.
Explore the following links to learn more about Erin’s work and the work of the other great researchers recently recognized.
Canadian Awarding ceremony of the L’Oréal-UNESCO For Women in Science fellowships
NSERC and L’Oréal-UNESCO For Women in Science Supplement
L’Oréal-UNESCO For Women in Science 2018: Erin McConnell
IUPAC Young Chemist
Congratulations to the Andres and Li Labs for a team effort in creating this Magic School Bus costume. The bus was driven to first place by Dr. Li as Ms. Frizzle and Dr. Andres as “Liz” the chameleon.
Take a look at this recent publication from the Li Lab in Angewandte Chemie International Edition. In this paper, we explore a novel signal amplification strategy termed DNAzyme feedback amplification (DFA). This method takes advantage of rolling circle amplification and RNA-cleaving DNAzymes for biosensing applications, with sensitivity improvements of 3-6 orders of magnitude when compared to conventional methods. -Suraj
Checkout this recent paper from the Li Lab in Scientific Reports, “Detection of DNA Amplicons of Polymerase Chain Reaction Using Litmus Test.” Here we report on a novel DNA detection method that combines the advantages of the polymerase chain reaction with the simplicity of a litmus test. The diagnostic capabilities of the platform is demonstrated using clinically validated stool samples from C.difficile infected patients. -Suraj
Yingfu as the “Crazy Cat Lady” and his gang of cats
Funding was recently announced to advance the Li lab’s research into rapid Legionella diagnostic technologies. Congratulations to our McMaster collaborators Dr. Carlos Filipe and Dr. John Brennan of the Biointerfaces Institute and industry partners TGWT Clean Technologies Inc., Cytodiagnostics and Mold and Bacterial Consulting Labs. Read more about it on the McMaster News website.
I am currently in my 3rd year as a PhD student in the Li Lab, and I am ecstatic to be a part of our efforts to develop colorimetric assays for a wide range of biologically relevant targets. I am currently working on the development of diagnostic assays that will enable detection of important cancer biomarkers.
-Sep
Sepehr Manochehry, a PhD candidate in his 3rd year, earned the coveted CIHR doctoral scholarship this year. He was ranked 6th nationwide, putting him in the top one percentile among more than 700 other applicants. His success and the focus of his research was recently featured in a news magazine article. Read it to gain a better understanding of what motivates hard-working graduates students like Sepehr. http://biochemrocks.freeflowdp.com/biochemrocks/2357984385961772?pg=23#pg23
