Andrés M
- Research Program Mentor
PhD at New York University (NYU)
Expertise
Biology, Creative Writing, Molecular genetics, Genomics, Yeast biology,
Bio
I have been working as a molecular geneticist in research labs across New York City for over 15 years. During that time, I have grown fond of model organism genetics and of nucleic acid biology (DNA and RNA). The topics that I have studied in depth include how RNA interference proteins influences aging and stress response in worms, how programmed DNA breaks shape genome evolution in yeast, and how the mammalian genome is dynamically folded and organized within the nucleus. Additionally, I am proponent of variation in it’s many contexts, and adore the famous Dobzhansky quote, “Nothing in Biology Makes Sense Except in the Light of Evolution.” Outside of science, I enjoy spending time with friends and family - hiking, dinner parties, and board games are popular hangout things we do. I also like to read fiction, go to the movie theater, cycling (the bicycle is a one of my favorite inventions), drawing, and creative writing (mostly poems and letter writing). I am currently working on a coffee table book about DNA, and I aspire to one day write a novella.Project ideas
10,000 Dog Genome Project
There is an open source dataset of genomes that are being sequenced from dogs throughout the world (see links below). Dog biology is cool, because there is so much variety of traits within a single species. Some of the interesting traits being studied include canine body size, coat variation, behavior, aging, cancer propensity, etc. One of the goals behind the 10K Dog Genome Project is to figure out how these traits are determined by their genes. Another goal is to help understand the evolutionary history of dogs. Currently there are dozens of publications using these data to address these topics and others. One possible independent project could be the analyses of this data to dive deeper into questions of dog genomics, e.g. are the mutation rates among different breeds similar or different, are there interesting regions of the genome that are evolving faster than other regions of the genome. This project would allow you to develop skills in understanding and manipulating genomic data and statistical tests. Another possible project could be to summarize the current findings and potential uses of this genomic data in a review article. Lastly, another possibility could be to design an experiment proposal based on some of the current findings. These latter two projects would allow you to develop skills reading scientific articles, critical/creative thinking, and scientific writing. This dataset is rich with many opportunities! https://research.nhgri.nih.gov/dog_genome/study_descriptions/study-dog10k.shtml http://www.dog10kgenomes.org/dog10k/introduction.html
Choose Your Own Synthetic Biology Adventure
The synthetic biology field was started roughly half a century ago, when genes from vertebrates were transferred into bacteria to manipulate the gene's protein production and isolation. Mammalian insulin was one of the notable first genes to inserted and expressed in bacteria to produce "synthetic" insulin, which is not only helpful to scale the production of insulin but also for diabetics who are allergic to previous insulin that was extracted from the pancreas of pigs. Since then there has been a wealth of synthetically engineered proteins and other molecules that make all kinds of inventions and medicines possible, like Impossible Burgers, CRISPR-based medical treatments, carbon capture and bioengineered fuels from microbes, palm oil, DNA-based computer storage systems, just to name a few. With a very very large repertoire of proteins that Nature has evolved to create and the tools that researchers have developed and continue to expand on, there are seemingly endless possibilities for synthetic biology solutions. For more examples, check out this open source academic journal - https://academic.oup.com/synbio and this review article - https://www.nature.com/articles/s41467-020-19092-2. There are many many Synthetic Biology projects that students can dream up. Here is the framework for one possible project. Propose a candidate protein or other macro-molecule that hasn't yet been synthetically engineered and would benefit from being produced in a synthetic manner. Describe the rationale, the motivation, and the genetic design process. Beyond these descriptions, you can also produce the finalized synthetic DNA sequence with annotations for important sequences, e.g. antibiotic selection markers, translation start and stop codons, gene(s) of interest, affinity purification tags. This project will give you a deep understanding of the structure and organization of genes and how their protein products function in the molecular world.
DNA Poetry Book
DNA is helical, stable, ubiquitous, generous, replicative... There are many things about DNA to know and to marvel about. The deeper one dives into the varied aspects of DNA, ones' wonder and appreciation for the molecule can reach greater heights. This project entails making a book of poems (12-24) on different topics of DNA. A few suggestions of the different DNA topics include: its historical discovery, DNA's different structural properties and organization, mitosis, meiosis, inheritance, cell-free DNA, sequencing and genomics, natural variation and evolution, disease, DNA repeats, extrachromosomal circular DNA, mitochondrial DNA, enhancers, centromeres, telomeres, DNA replication and repair, epigenetics (beyond the DNA), etc. If you can, find a typewriter for creating the final drafts and bind the book together using online tutorials as a guide.