PEPS 627/MBBE 627 Molecular Diagnostics: Principles and Practices" (3 Cr - 2 labs and 1 lecture; every year)
Instructor: Dr. Mohammad Arif
The goal of this course is to give the students a complete understanding about molecular diagnostics from experiment design, validation to peer-review publication. This is a graduate level course (lecture cum discussion and a lab) required active participation is expected along the way. In the lab, students will be working on molecular diagnostic project(s) to develop the diagnostic protocol(s); they will also be exposed to molecular techniques and bioinformatics. During the class, the latest technologies and principles will be discussed. The course will provide a new set of career skills; job opportunity and a career in molecular diagnostics and microbial forensics will also be discussed. I am also working to bring guest speaker(s) expert in diagnostics/microbial forensics, associated with federal agencies and/or diagnostic network. The ultimate aim is to publish the data generated during the lab classes. The course is not only designed for plant pathology students but also for the students from other disciplines, including entomology, microbiology, plant biology, molecular biology and food & animal sciences. This course has generated multiple peer-reviewed publications since 2017 (one article every year):
From Fall 2021 Class: Paper is submitted and under review in Scientific Reports
DeLude A, Wells R, Boomla S, Chuang S, Urena F, Shipman A, Rubas N, Kuehu DL, Bickerton B, Peterson T, Dobhal S, Arizala D, Klair D, Ochoa-Corona FM, Ali ME, Odani J, Bingham JP, Jenkins D, Fletcher J, Stack JP, Alvarez AM & Arif M. Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. Scientific Reports (communicated).
From Fall 2020 Class:
Domingo R, Perez C, Klair D, Vu H, Candelaria-Tochiki A, Wang X, Camson A, Uy JN, Salameh M, Arizala D, Dobhal S, Boluk G, Bingham JP, Ochoa-Corona F, Ali ME, Stack JP, Fletcher J, Odani J, Jenkins D, Alvarez AM, Arif M (2021). Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil. Scientific Reports, 11, 21948. doi.org/10.1038/s41598-021-01196-4
From Fall 2019 Class:
Ocenar J, Arizala D, Boluk G, Dhakal U, Gunarathne S, Paudel S, Dobhal S, Arif M (2019). Development of a robust, field-deployable loop-mediated isothermal amplification (LAMP) assay for specific detection of potato pathogen Dickeya dianthicola targeting a unique genomic region. PLoS ONE, 14(6):e0218868. doi.org/10.1371/journal.pone.0218868. Click here
From Fall 2017 Class:
Larrea-Sarmiento A, Dhakal U, Boluk G, Fatdal L, Alvarez AM, Strayer-Scherer A, Paret M, Jones J, Jenkins D, Arif M (2018) Development of a genome-informed loop-mediated isothermal amplification assay for rapid and specific detection of Xanthomonas euvesicatoria. Scientific Reports, 8:14298. doi.10.1038/s41598-018-32295-4; Click here
I encourage you to contact me, if you have any question(s) about the course.
The goal of this course is to give the students a complete understanding about molecular diagnostics from experiment design, validation to peer-review publication. This is a graduate level course (lecture cum discussion and a lab) required active participation is expected along the way. In the lab, students will be working on molecular diagnostic project(s) to develop the diagnostic protocol(s); they will also be exposed to molecular techniques and bioinformatics. During the class, the latest technologies and principles will be discussed. The course will provide a new set of career skills; job opportunity and a career in molecular diagnostics and microbial forensics will also be discussed. I am also working to bring guest speaker(s) expert in diagnostics/microbial forensics, associated with federal agencies and/or diagnostic network. The ultimate aim is to publish the data generated during the lab classes. The course is not only designed for plant pathology students but also for the students from other disciplines, including entomology, microbiology, plant biology, molecular biology and food & animal sciences. This course has generated multiple peer-reviewed publications since 2017 (one article every year):
From Fall 2021 Class: Paper is submitted and under review in Scientific Reports
DeLude A, Wells R, Boomla S, Chuang S, Urena F, Shipman A, Rubas N, Kuehu DL, Bickerton B, Peterson T, Dobhal S, Arizala D, Klair D, Ochoa-Corona FM, Ali ME, Odani J, Bingham JP, Jenkins D, Fletcher J, Stack JP, Alvarez AM & Arif M. Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. Scientific Reports (communicated).
From Fall 2020 Class:
Domingo R, Perez C, Klair D, Vu H, Candelaria-Tochiki A, Wang X, Camson A, Uy JN, Salameh M, Arizala D, Dobhal S, Boluk G, Bingham JP, Ochoa-Corona F, Ali ME, Stack JP, Fletcher J, Odani J, Jenkins D, Alvarez AM, Arif M (2021). Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil. Scientific Reports, 11, 21948. doi.org/10.1038/s41598-021-01196-4
From Fall 2019 Class:
Ocenar J, Arizala D, Boluk G, Dhakal U, Gunarathne S, Paudel S, Dobhal S, Arif M (2019). Development of a robust, field-deployable loop-mediated isothermal amplification (LAMP) assay for specific detection of potato pathogen Dickeya dianthicola targeting a unique genomic region. PLoS ONE, 14(6):e0218868. doi.org/10.1371/journal.pone.0218868. Click here
From Fall 2017 Class:
Larrea-Sarmiento A, Dhakal U, Boluk G, Fatdal L, Alvarez AM, Strayer-Scherer A, Paret M, Jones J, Jenkins D, Arif M (2018) Development of a genome-informed loop-mediated isothermal amplification assay for rapid and specific detection of Xanthomonas euvesicatoria. Scientific Reports, 8:14298. doi.10.1038/s41598-018-32295-4; Click here
I encourage you to contact me, if you have any question(s) about the course.
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It was one of the best course i took so far from the point of acquiring the practical skills of working on a molecular lab. I got to learn how to plan and execute the diagnostic projects. The theoretical portion provided all the information to need to understand the work we do in lab. it also enhanced the trouble shooting skills. Now i feel very confident about all the techniques i learnt during this class.
Student / Fall 2017
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We have really good lab experiments which were important to improve my lab skills. We also wrote a research manuscript which improved my writing skill.
Student / Fall 2017
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Everything and each class was worth.
Student / Fall 2017
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Thank you for providing us with this opportunity. Awesome class and team.
Student / Fall 2017
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