Genetically identical cells and organisms in the same environment show considerable differences in phenotype. Single cell study of a signaling system in S. cerevisiae (eg Yu et al. 2008) allowed us to quantify sources of phenotypic variation in signal and response (Colman-Lerner et al. 2005), and discover control strategies cells use limit the variation in these sources (Brent 2009, Andrews et al. 2016). One key contribution to variation is global difference in the amounts of protein dosage expressed from genes(Colman-Lerner et al. 2005). In S. cerevisiae and young adult C. elegans, differences in protein dosage cause differences in phenotypic expressivity and penetrance of mutant alleles and operationally define different physiological states (Mendenhall et al. 2016, Burnaevskiy et al. 2019). Some of the non-genetic variation is due to sporadic positive feedback driven events at the site of signal generation on the plasma membrane (Pesce et al., 2018). Deeper understanding of this non-genetic variation should allow, among other outcomes, better understanding of the effects of disease genes in the human population.
Experimentation in this lab has consistently emphasized development of new means (technology, experimental design, and doctrine) that we and other scientists can use to gain knowledge. Current projects include construction and use of "expression clamps", so called "well tempered controllers" of gene expression (WTCs). The first, WTC846, appropriates design principles and genetic elements from bacterial, eukaryotic and human built systems; combining autorepression, auxiliary repression, and positive feedback during induction to tune protein dosage while decreasing cell-to-cell variation in it. WTCs will allow us and others to control the amounts of expressed transgenes with great precision, and so find wide use. They will also allow direct experimental test of the effects of "normal" variation in protein dosage, a type of experiment not now possible. Current projects include other attempts, one based on deep neural networks and one on Augmented Reality (AR), aimed at accelerating the pace of scientific discovery.
Our work draws on different kinds of knowledge, and we conduct it with the benefit of strong collaborations. Key collaborations today are with the Alejandro Colman-Lerner lab at the University of Buenos Aires, Fabian Rudolf, Joerg Stelling, and coworkers at ETHZ Basel, Laura Boucheron and coworkers at NMSU Las Cruces, and William Lai and coworkers at an Augmented Reality startup company, IAS Machine. Lab members are encouraged to participate in advisory and "big picture" government policy activities, and to think broadly about how ongoing increases in biological knowledge and capability (and their own research) might inflect the course of human affairs. To this end, we also maintain an interaction with Alison Wylie (feminist philosopher of science) and coworkers at UBC Vancouver.
24 July 2019
Deep learning in Las Cruces
On July 23 and 24, Bill Peria, Roger Brent and collaborator Laura Boucheron led an intensive two day workshop on Deep Learning for Image Analysis at NMSI. The ~30 attendees included professors, postdocs, USDA scientists, a few graduate students, and a single undergraduate, from different science and engineering disciplines. Tutorials in Jupyter notebooks, written by Boucheron, taught participants Python coding to carry out basic image processing to build, train, and use convolutional neural networks within the Keras framework. Brent, Peria and Boucheron articulated what they considered to be key topics for near term research.
18 June 2019
Two wonderful recent undergraduates
The lab is enriched by the presence of Gabriella LaBazzo, a microbiology major, from Cody, Wyoming by way of Colorado State, and Karrington T. Ogans, a mathematics major, from Seattle having graduated from Gonzaga University. LaBazzo brings impressive infectious disease lab and field experience to her current work in and mammalian cells on Well Tempered Controllers. Ogans, who has been with us since February, is now working on deep neural networks and their possible use in epistemic support.
6 June 2019
O frabjous day! Single 5' intron sufficient for good reporter expression in worms
Scientific Reports has accepted for publication Crane et al., "In vivo measurements reveal a single 5’-intron is sufficient to increase protein expression level in Caenorhabditis elegans" for publication. During the scrambling early years of the recombinant DNA era and the start of the commercial biotech industry, it became widely known that inclusion of introns (Kaufman and Sharp, 1982, 1983, Kaufman, 1985) (the so called adenovirus tripartite leader, Logan and Shenk (1984) and polyadenylation sequences led to greater expression of recombinant proteins. The stimulation of gene expression by [even single] 5' introns was quickly found to operate in plants (Callis, Fromm, and Walbot, 1987). In C. elegans, very early work on transgenes by Andrew Fire and coworkers (Okema et al. 1993) showed introns aided gene expression and Fire included a three-intron construct in the clasical "C. elegans vector kit". But there was never a good reason to think that there was anything magical about three 5' introns, and the current work (BiorXiv 499459) shows that, as expected, there isn't. Work was started here by Bryan Sands and Alexander Mendenhall and finished in collaboration with them lab at the University of Washington.
12 May 2019
Actually, 4th lab supercomputer said Hello World already
As befits the nature of the work (to be funded by the Defense Threat Reduction Agency) the advent was a little stealthy... but the lab's 4th "supercomputer", Ghostwheel, has been up and running for awhile. Most of its work is calculations needed for computer vision. The most important part of Ghostwheel's brain is an NVIDIA RTX 2080; making him even more powerful than the first three lab computers.
10 March 2019
William Lai is a visiting scientist
Lab is enriched by William Lai. Lai is a senior and distinguished engineer, comes as a visiting scientist. Most of his early and formative industrial experience was with Microsoft. After more than a decade there, in 2008 he left Microsoft with a friend to co-found of 8ninths.com, an Augmented Reality agency in Seattle, where he handled engineering and technical development. Lai sold 8ninths successfully in late 2018. Lai will work on technology development projects underway here.