A5064067122- Genomics and Phylogenetic Studies
- Origins and Evolution of Life
- RNA and protein synthesis mechanisms
- Protist diversity and phylogeny
- Microbial Community Ecology and Physiology
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Photosynthetic Processes and Mechanisms
- Space Science and Extraterrestrial Life
- Chromosomal and Genetic Variations
- Photoreceptor and optogenetics research
- Evolution and Genetic Dynamics
- RNA modifications and cancer
- Peer-to-Peer Network Technologies
- Machine Learning in Bioinformatics
- Plant and Biological Electrophysiology Studies
- Caching and Content Delivery
- Planetary Science and Exploration
- Advanced Data Storage Technologies
- Astro and Planetary Science
- Microbial Metabolic Engineering and Bioproduction
- Amino Acid Enzymes and Metabolism
- Bacterial biofilms and quorum sensing
- Mitochondrial Function and Pathology
- RNA regulation and disease
Oberlin College
2013-2025
Blue Marble Space
2018-2024
Blue Marble Space Institute of Science
2018-2024
Princeton University
2012-2014
Georgia Institute of Technology
2012-2014
University of Washington
2009-2013
NASA Astrobiology Institute
2013
University of South Florida
2012
Seattle University
2010
Carnegie Mellon University
2005
Pseudomonas aeruginosa, the principal pathogen of cystic fibrosis patients, forms antibiotic-resistant biofilms promoting chronic colonization airways. The extracellular (EPS) matrix is a crucial component that provides community multiple benefits. Recent work suggests secondary messenger, cyclic-di-GMP, promotes biofilm formation. An analysis factors specifically expressed in P. aeruginosa under conditions elevated c-di-GMP, revealed functions involved production and maintenance matrix. We...
The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic architecture with extensive genomic variation. During sexual development, expressed, somatic is whittled down to genic portion a small fraction (∼5%) its precursor “silent” germline micronuclear by process “unscrambling” fragmentation. tiny “nanochromosomes” typically encode single, protein-coding genes (a portion, 10%, 2–8 genes), have minimal noncoding regions, are differentially amplified...
Abstract Many decades of experimental and theoretical research on the origin life have yielded important discoveries regarding chemical physical conditions under which organic compounds can be synthesized polymerized. However, such often seem mutually exclusive, because they are rarely encountered in a single environmental setting. As such, no convincing models explain how living cells formed from abiotic constituents. Here, we propose new approach that considers within global context Hadean...
Abstract The RNA World is one of the most widely accepted hypotheses explaining origin genetic system used by all organisms today. It proposes that tripartite DNA, RNA, and proteins was preceded consisting solely which both stored information performed molecular functions encoded information. Current research into a potential revolves around catalytic properties RNA-based enzymes, or ribozymes. Well before discovery ribozymes, Harold White proposed evidence for precursor world could be found...
The triosephosphate isomerase (TIM) barrel protein fold is a structurally repetitive architecture that present in approximately 10 % of all enzymes. It generally assumed this ubiquity modern proteomes reflects an essential historical role early protein-mediated metabolism. Here, we provide quantitative and comparative analyses to support several hypotheses about the importance TIM architecture. An information theoretical analysis structures supports hypothesis could arise more easily by...
All life on Earth is unified by its use of a shared set component chemical compounds and reactions, providing detailed model for universal biochemistry. However, this notion universality specific to known biochemistry does not allow quantitative predictions about examples yet observed. Here, we introduce more generalizable concept biochemical that akin the kind found in physics. Using annotated genomic datasets including an ensemble 11,955 metagenomes, 1,282 archaea, 11,759 bacteria, 200...
The availability of genomic and proteomic data from across the tree life has made it possible to infer features genome proteome last universal common ancestor (LUCA). A number studies have done so, all using a unique set methods bioinformatics databases. Here, we compare predictions eight such measure both their agreement with one another consensus among them. We find that some LUCA show strong others, but no individual study shares high or even moderate degree similarity any other study....
Organisms represented by the root of universal evolutionary tree were most likely complex cells with a sophisticated protein translation system and DNA genome encoding hundreds genes. The growth bioinformatics data from taxonomically diverse organisms has made it possible to infer properties early life in greater detail. Here we present LUCApedia, (http://eeb.princeton.edu/lucapedia), unified framework for simultaneously evaluating multiple sets related Last Universal Common Ancestor (LUCA)...
The origin and early evolution of life is generally studied under two different paradigms: bottom up top down. Prebiotic chemistry Earth geochemistry allow researchers to explore possible scenarios. But for these "bottom-up" approaches, even successful experiments only amount a proof principle. On the other hand, "top-down" research on evolutionary history able provide historical account about ancient organisms, but unable investigate stages that occurred during just after life. Here, we...
Current evidence suggests that some form of cellular organization arose well before the time last universal common ancestor (LUCA). Standard phylogenetic analyses have shown several protein families associated with membrane translocation, transport, and bioenergetics were very likely present in proteome LUCA. Despite these systems emerging prior to LUCA, extant archaea, bacteria, eukaryotes significant differences infrastructure molecular functions support it, leading researchers argue true...
The RNA world hypothesis posits that the earliest genetic system consisted of informational molecules directed synthesis modestly functional molecules. Further evidence suggests it was within this RNA-based life developed ability to synthesize proteins by translating code. Here we investigate early development translation through an evolutionary survey protein architectures associated with modern translation. Our analysis reveals a structural expansion immediately following and well before...
All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been complex cellular organism. A new study by Moody et al. shows that this ancestor was not only cell, but also lived within microbial ecology likely inhabited other cells.
We introduce the concept of metaconsensus and employ it to make high confidence predictions early enzyme functions metabolic properties that they may have produced. Several independent studies used comparative bioinformatics methods identify taxonomically broad features genomic sequence data, protein structure pathway data in order predict physiological were present early, ancestral life forms. But all such carry with them some level technical bias. Here, we cross-reference results these...
Abstract The emergence of cellular organisms occurred sometime between the origin life and evolution last universal common ancestor represents one major transitions in evolutionary history. Here we describe a series artificial simulations that reveal close relationship cellularity, metabolism, richness environment. When environments are rich processing energy, resource digital require to both process their genomes replicate, populations evolve toward state non-cellularity. But when energy is...
In this study, we used a computational approach to investigate the early evolutionary history of system proteins that, together, embed and translocate other across cell membranes. Cell membranes comprise basis for cellularity, which is an ancient, fundamental organizing principle shared by all organisms key innovation in evolution life on Earth. Two related requirements cellularity are that able both into One accomplishes these tasks signal recognition particle (SRP) system, core protein...