Using the genome, transcriptome and proteome to better understand species: from Homo sapiens to Homarus americanus
field of genetics encompasses genomics, transcriptomics and proteomics and entails
understanding the role of organisms' genes. These three omes along with numerous
genetics based tools including next generation sequencing platforms and ultrasensitive
protein assays can be utilized to inform and expand our understanding of different
species and solve a multitude of problems. Usin... read moreg two different model organisms (Homo
sapiens and Homarus americanus), we utilized genomic, transcriptomic and proteomic data
to address the objectives of our projects. For both projects, we used the transcriptome
in different ways to address our goals. For the first project, we used the neonatal
transcriptome to independently inform us about the proteome. For the second project, we
used the American lobster transcriptome as a reference for assembling the de novo
genome. The aim of the first project was to determine if we could detect oral feeding
readiness from neonatal saliva. A two-tiered approach was taken to address this goal.
First, research was conducted to translate a previously identified transcriptomic panel
(informative of oral feeding readiness) into a rapid proteomic platform to provide
objective, near real-time assessment of oral feeding skills, to better inform care and
improve neonatal outcomes. Assays for proteins involved in sensory integration, hunger
signaling and facial development were developed. This study provided the foundation for
the development of an informative rapid proteomic platform to assess neonatal oral
feeding maturation. Simultaneously, an RNA sequencing platform was used to advance the
development of feeding assessment tools by reviewing the entire human transcriptome
using a high-throughput and quantitative approach. This work was undertaken to better
understand the disrupted developmental patterns in the premature newborn. Moreover, we
conducted a supplementary study to identify reliable reference genes to use for
normalization of transcriptomic data in neonatal salivary diagnostics. These projects
were all conducted in neonatal saliva and helped elucidate the complexities involved in
neonatal oral feeding maturation with the help of transcriptomic and proteomic data. The
goal of the second project was to hone my bioinformatics skills and provide a complete
American lobster genome and in turn, a foundation for crustacean genetics studies. Among
crustaceans, the American lobster is an iconic species that is integral to many marine
ecosystems and is an important commercial fishery in the Northwest Atlantic. By using
the sequenced transcriptome as a reference for assembling the de novo genome we were
able to provide the first complete American lobster genome. We annotated approximately
37,000 genes from the genome and 24,000 from the transcriptome. A 70% to 80% concordance
between the genome and transcriptome was observed signifying complete sequencing of the
genome. Utilizing the genomic, transcriptomic and proteomic information collectively, we
were able to study the smallest of humans to the largest of crustaceans. Not only did we
use this approach to address challenges in the clinical setting but also in the
commercial fishing industry. Hence, it is important to consider the genome,
transcriptome and proteome simultaneously and how they can help better inform each other
to address numerous genetic enigmas.
Thesis (Ph.D.)--Tufts University, 2017.
Submitted to the Dept. of Genetics.
Advisors: David Walt, and Jill Maron.
Committee: Mitch McVey, Diana Bianchi, and Jonathan Garlick.
Keyword: Genetics.read less