Application deadline March 24: Rolling review begins March 17
Course Subject:
Mobile genetic elements (MEs) can mediate rapid adaptation by introducing genes that encode novel functions related to pathogenesis, symbiosis and metabolism into host cells. MEs, and the accessory genes they carry, are as varied as the hosts and niches they are found within. Fuller understanding of the dynamics, constraints and consequences of ME movement will require interdisciplinary research merging computational and experimental approaches. This hands-on course will integrate laboratory experiment with quantitative bioinformatic analysis, providing students from diverse disciplinary backgrounds with new experience and skills that will assist them in developing rigorous, quantitative research in microbial evolution and ecology.
Course Faculty:
Joanne Emerson (UC Davis), Benjamin Good* (Stanford U.), Roberto Kolter (Harvard Medical School), Honour Mc Cann* (MPI-EB), Richard Neher (U. Basel ), Boris Shraiman (KITP/UCSB), and Paul Turner (Yale U.)
*Course Director
Guest Lecturers (partial list):
The summer course is closely linked to the concurrent KITP program Horizontal Gene Transfer and Mobile Elements in Microbial Ecology and Evolution. Course participants will attend the program's daily research seminars as part of the course curriculum. Students and lecturers will also have frequent opportunities for less formal interactions. Confirmed program participants include Aude Bernheim (Pasteur Inst.), Devaki Bhaya (Carnegie Science/Stanford U.), Allison Carey (U. Utah), Ilana Brito (Cornell U.), Daniel Fisher (Stanford U.) Nandita Garud (Stanford U.), Graham Hatfull (U. Pittsburgh), Daniel Huson (U. Tübingen), Eugene Koonin (NCBI), Michael Laub (MIT), Katie Pollard (Gladstone Inst., UCSF), Martin Polz (U. Vienna), Paul Rainey (MPI-EB), Eduardo Rocha (Inst. Pasteur), Julia Salzman (Stanford U.), and Erik van Nimwegen (U. Basel).
Course Structure
The course is 5 weeks long, and runs concurrently with the KITP Program Horizontal Gene Transfer and Mobile Elements in Microbial Ecology and Evolution. Students will begin with a bootcamp on basic wetlab techniques, then break into project groups for the first section of wetlab projects. After wrapping up wetlab data collection and preparing samples for sequencing, students break for a drylab bootcamp. Students will then join and complete a drylab project. During this period, sequencing for wetlab projects will be completed. During the last week, students will analyse the data from their wetlab projects, and present their findings to the program.
The experimental projects are led by instructors and TAs working closely with groups of 4-5 students. Additional guest lectures and training modules will be provided throughout the course. Students regularly attend morning lectures offered as part of the KITP Program, then head off for lab work in the afternoon and evening. Students are welcome to join visiting lecturers and program participants for tea breaks and evening BBQs at the Munger Physics Residence. Weekends are open for students to explore and enjoy the many recreational opportunities in the Santa Barbara area.
Accommodations, Fees, and Financial Assistance
There is no tuition, lab fee, or room and board fee. Admitted students are provided with double-occupancy rooms in UCSB student apartments and a 19-meal plan at campus dining commons. A limited number of single rooms are available for a $2064 supplement. Students who need financial assistance with travel expenses can request it in the application form; financial need does not affect an applicant's chances of admission.
Experimental Projects
Evolution of bacterial genomic structure (Richard Neher and Marco Molari)
Bacteria exchange genetic material horizontally, duplicate DNA, delete parts or invert stretches of their genome resulting in complex patterns of genetic diversity. Despite the overall diversity and structural complexity, the order of essential genes in bacterial genomes tends to be highly conserved and most of the horizontally acquired diversity is concentrated in hot-spots. In this project, we will construct genome graphs of groups of recently diverged bacteria (specific sequence types) using PanGraph. PanGraph is a tool to detect shared homologous sequences between a large number of genomes and summarize it in a concise graph structure. Using this graph, we will quantify the rates at which horizontal processes add or exchange genes and will detect aforementioned hot-spots and characterize their sequence repertoire.
___________________________________________________________________________________________________________
Examining G x G x E interactions in evolution of bacterial-pathogen resistance to therapeutic phages (Paul Turner)
This project examines three lytic phages of Pseudomonas aeruginosa (PsA) that have been used successfully in FDA-approved emergency therapy to treat antibiotic-resistant pulmonary infections in humans. Each phage infects PsA using a different cellular receptor, and can select for host bacteria to evolve phage-resistance that either reduces virulence or switches hosts to become antibiotic sensitive (i.e., phage induced trade-offs). In week 1, students will challenge the phages to infect a collection of PsA strains that are cultured in different environments, to test how the culture conditions impact the spectrum of isolated phage-resistant mutants. These ‘rescue’ mutants will then be submitted for whole-genome sequencing, to analyze the loci underlying evolved phage-resistance. Week 2 will involve analyses of the genomic results. In addition, students will conduct phenotypic (growth) assays on the mutant isolates using automated spectrophotometers (microplate readers) and R programs that infer quantifiable bacterial traits, to conduct rigorous genotype-phenotype analyses. The overall goal is to generate a large dataset of novel results that will inform phage-bacteria-environment (G x G x E) interactions, useful for future emergency patient treatment leveraging phage-induced trade-offs in this important bacterial pathogen system.
___________________________________________________________________________________________________________
Dynamics of ICE movement in bacterial populations (Elena Colombi and Honour Mc Cann)
Integrative and conjugative elements (ICEs) are large, self-transmissible mobile elements that mediate the movement of ecologically significant genes across even distantly related membes of the Pseudomonas syringae species complex. Excision, conjugal transfer from the donor, and site-specific integration into the recipient can occur within fifteen minutes in vitro. Newly acquired ICEs can replace or recombine with ICEs already present in recipient cells, generating novel chimeric elements. ICEs are known to vector genes with functions associated with antibiotic resistance, pathogenicity and symbiosis, bacteriocin synthesis and more. For this project, we will start by performing transfer and competition experiments to assess the host range and fitness contributions of ICEs in different recipient strains. We will then set up and sequence a serial passage experiment to quantify rates of ICE transfer in mixed populations. Students will explore whether ICE proliferation is linked to their contributions to host fitness, or is selfish in nature.
___________________________________________________________________________________________________________
Rates of Horizontal Gene Transfer and Transposition in Non-Growing Bacteria (Roberto Kolter and Benedek Facskó)
Comparative genomics led to the insight that horizontal gene transfer events are the prevalent mode of bacterial genome evolution. We know much about the modes of horizontal gene transfer, i.e., transformation, conjugation, transduction, etc. Most of the past studies that measured the rates of these processes utilized fast growing populations. Yet, we know that in natural settings, bacteria seldom encounter conditions propitious for fast growth. In this project, we will quantitate the rates of transduction in non-growing or very slow-growing bacterial populations. As a complement, we will also follow the dynamics of mobile genetic elements in non-growing cells. In addition, we'll explore the ecological implications of the little-explored phenomenon of abortive transduction.
___________________________________________________________________________________________________________
Spatial patterns of soil viral communities (Joanne Emerson)
Students will investigate spatial structuring of soil viral communities to identify patterns and drivers of community composition. The project will begin with sampling soil and wetland environments in the area, then enriching for viral communities via filtration. Students will extract DNA from filtered and unfiltered samples, then sequence the viromes and metagenomes using MinION and Illumina platforms. Viral genomes will then be identified, and viral community composition will be compared to identify ecological differences along the sampled gradients. Finally, students will look for evidence of horizontal transfer by searching for integrated prophages in microbial genomes and 'host' genes in viromes.