2015 JGI Users Meeting Notes

Interested in watching any of these talks?  See this webpage!


Jack Gilbert -- Genome-Enabled Flux Balance Metabolic Networks Form Periodically Flooded Soils

• Presented an array of studies across many different microbial communities
• environmental microbes have roughly a 35 year lab to major climate changes
• Cyanobacteria can metabolize nitrogen into amonium which has been show to be useful in sphagnum moss
• bacteria can protect against allergies.  Adding clostridium into mouse will alleviate allergenic symptoms
• added clostridium to a young man who had really bad allergies.  Comparisons to other family members without allergies is in progress
• also doing this experiment on dolphins because it is easier to control their environment
• microbes can contribute to you being fat or skinny
• circadian rhythms in the gut genes and microbes looks to be very important
• microbes in roots also have circadian cycles 
• your house takes on your microbiome
• dogs increase the similarity of couple's microbiomes

Francis Martin -- Harnessing Genomics for Understanding Tree-Microbe Interactions in Forest Ecosystems

• we know very little about fungi affect the carbon cycle
• 4 major groups of fungi in most forest ecosystems:  white rotters, brown rotters, litter soul decayers, and ectomycorrizal
• he studies mycorrhizal fungi and their symbiotic toolkit
• mycorrhizal symbiosis has evolved independently several time!
• ectomycorrizal fungi (EMF) have reduced complement of plant cell wall degrading genes compared to ancestors
• small proteins from EMF are secreted and land on plant cells
• Look at Platt paper for JAZ interaction (PNAS).  Missp7 binds to JAZ and prevents the immune response in the plant
• each symbiosis event has developed a unique set of effectors

Joan Bennett -- Do Fungi have a 'Volatome'?

• aflotoxins can cause cancer in small doses
• mycotoxins may cause sick building syndrome
• volatile organic compounds (VOCs) are things that we can smell and are frequently made by fungi
• using arabidopsis and flies as models for testing the effects of these compounds
• flies exposed to c-8 VOCs acted similarly to model flies for Parkinson's disease
• VOCs in the fungal microbiome of humans are likely responsible for attracting mosquitoes

Susanna Theroux -- Marsh Madness: Microbial Communities Driving Greenhouse Gas Cycling in Coastal Wetlands

• wants to link wetland microbes with carbon emissions
• methanogens break down carbon into methane
• wetlands produce a lot of methane
• microbes might be useful in minimizing methane production compared to carbon storage
• more methanogens yield more methane

Antonis Rokas -- Evolution of Fungal Chemodiversity

• fungal metabolism
• asks how did chemo diversity originate and why is chemo diversity clustered
• toxicity clusters are likely driven by genetic linkage (ie butterflies)
• mined metabolic databases for genes that are clustered and genes that are not and measured toxicity.  Clustered genes are more toxic
• tissue specific expression in humans and mammals is the equivalent of clustering in fungi
• this implies that the position of two genes in the fugal genome give information about how they interact in humans (ie those two genes are likely to be expressed in the same tissue)

Rotem Sorek -- The Immune System of Bacteria

• crisper is the immune response in bacteria for phages
• the cas proteins find phage DNA in the cell and insert it into the next spacer
• crisper is in only ~40% of bacteria.  How do other bacteria fight phage?  The only other known mechanism is restriction enzymes.  Can we find new immune systems in bacteria?
• immune system signatures:  rapidly evolving, high horizontal gene transfer
• found the BREZ system in B. cereus!  Found in 10% of bacteria.  We don't understand the mechanisms yet
• phages have anti-defense systems.  Ergo it would be best for bacteria to have multiple defense systems

Phil Hugenholtz -- Back from the Dead:  The Curious Tale of the Predatory Cyanobacterium Vampirovibrio chlorellavorus

• these bacteria suck host cells dry!
• falls in Cyanobacteria clade
• contains a type-IV secretion system partially found on plasmids
• non photosynthetic (unlike most Cyanobacteria)

Stephen Wright -- Comparative and Population Genomics in the Brassicaceae:  Understanding Genome-Wide Natural Selection

• evolution can go backwards.  For example, Y chromosome degeneration in humans.
• many plants that undergo whole genome duplication revert to diploid
• there is evidence in Arabidopsis that a long time ago it had a whole genome duplication event
• possible explanations:  passive constituency of redundancy, inefficient selection, differential adaptation
• there is limited evidence contrary to popular theory that selfing or limited recombination leads to a high density of deleterious mutations and evolutionary dead-ends
• capsella rubells is a model for this phenomenon
• ploidy effects the efficiency of natural selection
• higher ploidy can weaken efficacy of natural selection
• ploidy combined with transition to selfing increases rate of deleterious mutation accumulation
• plant sex chromosomes are younger than mammalian sex chromosomes

Steve Briggs -- Protein Regulatory Networks

• see Walley et al. PNAS 2013!

Susan Lynch -- The Microbiome--A New Frontier in Human Health

• increase in asthma cases in children in US and Australia
• asthma is mostly an environmental disease (ie not so much genetic)
• now people have far less environmental exposure
• Americans spend about 90% of their time indoors
• vaginal born children have different microbiome than c-section born children.  And they are less likely to have asthma.
• lactobacillus keeps airways of mice challenged with dust open like normal airways
• see Fuijmura et al PNAS January 2014
• WHEALS study
• allergenic children often develop asthma