I seek to foster a better understanding of molecular biology, towards the end of engineering living systems to solve real world problems. This passion drives my research interests, teaching, and other activities.
Synthetic Biology and iGEM
The emerging discipline of synthetic biology holds tremendous potential for both basic research and innovative applications. In some ways, synthetic biology is a more ambitious expression of the same impulse behind most contemporary biotechnology; engineering entire pathways instead of single proteins and enzymes. However, this field goes beyond most traditional efforts in both scope and approach.
Synthetic biology also represents a revolution in terms of who can access drive research efforts. Every year, important advancements in this field are made by teams of undergraduates competing in the International Genetically Engineered Machine competition (iGEM). The iGEM competition is a new and exciting model for scientific research and technological development. I have been involved in iGEM for many years (since 2005), most recently as the iGEM coordinator at Alma college and a faculty mentor for the team. Alma’s first iGEM team, fielded in 2019, brought home a silver medal in the competition - one of the best results in the Midwest (https://2019.igem.org/Team:Alma). We improved upon this result and earned a Gold Medal in the midst of the COVID pandemic the following year (https://2020.igem.org/Team:Alma) To learn more about the wonderful iGEM competition and see examples of team projects from years past, please visit http://www.igem.org
Often, parts of macromolecules that appear to be weakly conserved are ignored or not considered a priority for analysis. However, many proteins and RNA molecules make functionally important and sequence specific contacts with other macromolecules. For some of these contacts, they will not be conserved individually, but the pairs of residues will more commonly be found together. Identification of these co-evolved pairs can be done through bioinformatic means.
I have developed new software tools to more rigorously predict inter-molecular interactions and co-evolution. These new tools will be trained upon molecules involved in translation, such as tRNAs, amino-acyl tRNA synthetases (AARS), and ribosomal proteins, so that we may better understand this dynamic process. This is critical for efforts to manipulate bacterial gene expression. For example, this research may lead to new ways to re-engineer tRNA-AARS pairs and expand the types of proteins that can be created in a cell.
For more information about this software, my research interests or other professional information, please visit my other site at: http://www.bioinformatics.org/aces/
- Ph.D., Molecular and Cellular Biology, Stony Brook University (Karzai Laboratory)
- B.Sc, Biotechnology, Rutgers University (Cook College, now SEBS)
.. trained in molecular biology and biochemistry. I focus on learning concepts and connections, engaging students with real-world problems and their synthetic biology solutions.
My career at Alma began in
I'm an expert in
- Research in Synthetic Biology and the International Genetically Engineered Machine competition (iGEM).
- Gene expression control in bacteria.
- Co-evolution and related Bioinformatics (programming in Java)
Camenares, D (2020) ACES: A Co-Evolution Simulator Generates Co-varying Protein and Nucleic Acid Sequences. Journal of Bioinformatics and Computational Biology. http://doi.org/10.1142/S0219720020500390
Virtual Vnat Conference, February 2nd, 2021 (Presentation) “pSB1C3 replication in Vibrio natriegens: An Origin Story” Archived here: https://sites.williams.edu/vnatconference/
American Society for Biochemistry and Molecular Biology Catalyst Conversation @ Albion College, March 7th, 2020 (Co-Presentation with Dr. Brian Doyle)
“MiGEM: Integrating science and the humanities through synthetic biology to foster personal connections in biochemistry.”
American Society for Biochemistry and Molecular Biology Annual Meeting, April 4th, 2019 (Poster)
“Simulating protein and nucleic acid sequence co-evolution”
Other recent accomplishments:
Mentored the Alma College iGEM team in 2019 (silver medalist) and 2020 (gold medalist)
Mentored the Kingsborough Community College iGEM team in 2016 and 2017 (bronze medalist)