STEMinar alternative - Virtual Seminar “Conserving California: Applying Whole Genome Sequencing in the California Conservation Genomics Project (CCGP)” Recorded on May 11, 2022. Daniel Oliveira, M.S. - Mini-core Technichian at UCLA; Courtney Miller, Ph.D. - Project Manager for CCGP at UCLA; Ariele Hanel, Ph.D. - Director of Applications and Support at seqWell
Questions
How does UCLA ensure that tissue samples are taken from animals in an ethical manner that does not result in the death or significant injury of animals that tissues are being taken from?
What support is allotted to those who do not understand or have a unique occurrence that concerns the pipeline organizational structure?
How is DNA sequenced after pooling and how exactly does the machine determine the presence of adapters?
How are the pipets in the machine cleaned?
Reflection
New concepts discussed include the phrasing of a pipeline organizational structure, the concept of pooling genetic information together with distinctions between species being determined through tagging as well as the application of using batched wells for DNA sequencing instead of ELISA testing. Decerning tagging and pooling, it was learned that i7 barcoding adapters are applied to specific individual genomes of which after i5 barcoding adapters were added to distinguish a pool in order to assure distinction as well as greater efficency in collective amplification (replication) in a plexWell system which is less expensive than conventional methods in library stage of DNA/RNA sequencing as amplification occurs after pooling. As such, it was used for UCLA’s CCGP project which aimed to create a high quality whole genome data set for comparison of further research in the influence of climate change and other factors and species diversity and viability. One of the tasks of the project manager was to develop a pipeline for decision making decerning what tissue samples would be tested, where they would be tested, etc. combining consideration of lab steps and decision making so as to be of greater clarity. In this process, a tissue sample would be taken followed by preparation/processing by human hand or by a machine, being Eppendorf epMotion robot, of which increases the time efficiency at which samples are processed through batching them in wells. However, there was some noticeable error in some instances due to density of polysaccharides in samples that resulted in dripping from the caps of pipets. Thereafter, they would be inserted into pools/libraries for DNA sequencing of which processing and further steps would be performed by a Mini-core Technician.
The occupation of the Mini-core Technician may be preferable in that one would be monitoring and performing light repetitive tasks requiring a steady hand and attention while also contributing to the knowledge of the genome of species in order to determine strategies that can be used to ensure integrity of populations though one would be likely to decline it since it does not actively incorporate direct interaction with animals in the admiration of their phenotypic traits. As for a project manager, it would be preferable to be able to organize and adapt plans in order to help meet similar goals, though it is not considered for reasons listed previously. The use of machines to aid in batch assessment of solutions may be applicable in other fields such as with ELISA testing, analysis of other organic materials such as urine or blood and so on. The use of pooling may also be applicable in such but due to lack in connectedness and variety as is with DNA, this holds dought.
Questions
How does UCLA ensure that tissue samples are taken from animals in an ethical manner that does not result in the death or significant injury of animals that tissues are being taken from?
What support is allotted to those who do not understand or have a unique occurrence that concerns the pipeline organizational structure?
How is DNA sequenced after pooling and how exactly does the machine determine the presence of adapters?
How are the pipets in the machine cleaned?
Reflection
New concepts discussed include the phrasing of a pipeline organizational structure, the concept of pooling genetic information together with distinctions between species being determined through tagging as well as the application of using batched wells for DNA sequencing instead of ELISA testing. Decerning tagging and pooling, it was learned that i7 barcoding adapters are applied to specific individual genomes of which after i5 barcoding adapters were added to distinguish a pool in order to assure distinction as well as greater efficency in collective amplification (replication) in a plexWell system which is less expensive than conventional methods in library stage of DNA/RNA sequencing as amplification occurs after pooling. As such, it was used for UCLA’s CCGP project which aimed to create a high quality whole genome data set for comparison of further research in the influence of climate change and other factors and species diversity and viability. One of the tasks of the project manager was to develop a pipeline for decision making decerning what tissue samples would be tested, where they would be tested, etc. combining consideration of lab steps and decision making so as to be of greater clarity. In this process, a tissue sample would be taken followed by preparation/processing by human hand or by a machine, being Eppendorf epMotion robot, of which increases the time efficiency at which samples are processed through batching them in wells. However, there was some noticeable error in some instances due to density of polysaccharides in samples that resulted in dripping from the caps of pipets. Thereafter, they would be inserted into pools/libraries for DNA sequencing of which processing and further steps would be performed by a Mini-core Technician.
The occupation of the Mini-core Technician may be preferable in that one would be monitoring and performing light repetitive tasks requiring a steady hand and attention while also contributing to the knowledge of the genome of species in order to determine strategies that can be used to ensure integrity of populations though one would be likely to decline it since it does not actively incorporate direct interaction with animals in the admiration of their phenotypic traits. As for a project manager, it would be preferable to be able to organize and adapt plans in order to help meet similar goals, though it is not considered for reasons listed previously. The use of machines to aid in batch assessment of solutions may be applicable in other fields such as with ELISA testing, analysis of other organic materials such as urine or blood and so on. The use of pooling may also be applicable in such but due to lack in connectedness and variety as is with DNA, this holds dought.