Areas of Research
Dr. Ruby’s lab has a continuing interest in bacterial symbiosis with animals. They work closely with their collaborators in Dr. Margaret McFall-Ngai’s group to investigate the Vibrio fischeri-sepiolid squid light-organ association as a model for beneficial bacteria-host interactions. They have laid the foundation for understanding the role of bacterial signals in triggering the differentiation of host tissues during development, and the function of quorum signaling and bioluminescence in regulating symbiosis. To reach their goals, the Ruby lab has spearheaded the development of molecular genetics in V. fischeri, and produced the first 20 genome sequences for this bacterium. They have helped their collaborators to produce the first genome-scale metabolic model, and to push transcriptomics assays down to as few as 100,000 cells. These tools have provided a window into the step-wise changes in gene expression that drive the development of a persistent beneficial microbial association. Their current research activity is focused on applying systems biology to understanding how sequential signaling cascades, and nutrient-manipulation can produce rhythmic patterns of bacterial activity that underlie the persistence of long-term microbial symbioses.
The Ruby lab’s current research directions include:
- a broad-based approach to analyzing how sequential signaling cascades and nutrient manipulation produce rhythmic patterns of bacterial metabolism that underlie the association’s persistence,
- new analytical and imaging approaches to describe novel vehicles and pathways of signaling between the symbiont and its host, and
- comparative and functional genomics to discover principles controlling population-level interactions among symbionts.
View Ruby CV 
Announcements
Postdoctoral Position in McFall-Ngai and Ruby Laboratories (posted 10-15-16)
Mentors: Margaret McFall-Ngai, Ned Ruby, Janna Nawroth
A postdoctoral position is available at the Pacific Biosciences Research Center (PBRC) working at the interface of microbiome, biophysics, and molecular biology studies. Specifically, the project will investigate the role of ciliary actuation, sensing and signaling in the squid-vibrio symbiosis. The candidate will employ and develop a variety of biological imaging techniques and analysis tools and, in collaboration with the Kanso group at USC, perform computational modeling studies to unravel the biology and biophysics of bacteria-cilia interactions. The project will be conducted at PBRC’s Kewalo Marine Laboratory in Honolulu. Ph.D. degree required. Expertise in microbiology, molecular biology, biological imaging, signal processing, and/or biophysics desired. The candidate will work with biologists, physicists and mathematicians as a part of grant from the NSF INSPIRE Program, which seeks to promote interdisciplinary research. The candidate will be expected to work both independently and in a team, and to acquire new skills and knowledge outside his or her area of expertise.
Position available immediately. Applications should include a CV and statement of research and career interests. The materials can be sent to the mentors, McFall-Ngai (This email address is being protected from spambots. You need JavaScript enabled to view it.), Ruby (This email address is being protected from spambots. You need JavaScript enabled to view it.) and Nawroth (This email address is being protected from spambots. You need JavaScript enabled to view it.).
Animal-Microbe Symbioses Gordon Conference
