Here are some notes from a few of the speakers at the JGI Users meeting in California. In general the speakers were fantastic. Some general themes of the conference include: single-cell genomics, synthetic biology, fungal metagenomics, and metabolics. A person take-home message for me was the need for creative biological solutions to common issues that the human race currently faces or will face in the near future.
Mark Ackermann (opening keynote) – A
Single Cell Perspective on Bacterial Interactions
- Focused on phenotypic heterogeneity, when identical cells
have different functional profiles.
- Most genes don’t have clonal variation but in the ones
that do how is that heterogeneity important for the community.
- Salmonella is an example of phenotypic heterogeneity. One cell type causes inflammation and one
uses the inflammation response to reproduce and cause full infection.
- Different cell types survive better in different
environmental conditions.
- Another example of phenotypic heterogeneity is in alpine
lakes where there are generally large amounts of ammonium that bacteria can use
as a nitrogen source. However, there are
some cells that fix their own nitrogen in the event that ammonium runs out.
- preliminary data show that neighboring cells are more
likely to be of the same cell type.
Mary Berbee –
Pectinases link Early Fungal Evolution to the Land Plant Lineage
- Sequenced early divergent fungal groups.
- The relationship between the early branching groups is
still poorly resolved.
- Showed some cool trees where she had overlaid two trees to
highlight difference between the two. I
would like to know what software she used to do this.
- Her trees were based on whole genomes but I’m not sure how
she built them.
Rytas Vilgalys –
Understanding the Forest Microbiome: A
Fungal Perspective
- Oak and pine share many fungi while populus has more
different fungi.
- Soils from the same region are likely to share the same
fungi.
- Populus of different genotypes do not assembly different
fungi. At least not nearly as different
as fungi from different regions.
- They have isolated ~1,800 fungal isolates. These isolate represent only ~15% of the
isolates that are likely populus endophytes.
- Many fungal isolates stimulate plant growth.
- They are re-inoculating these isolates to confirm they are
endophytic.
- Mortierella elongata is an isolate that stimulates plant
growth in populus and Arabidopsis thaliana.
- M. elongata also harbors bacterial symbionts
(Glomeribacter which are known to affect lipid fermentation and is a sister to
Burkholderia. These bacteria cannot be
cultured possibly because they rely so heavily on the host for nutrients).
- M. elongata migrate to the roots.
- Different genes are expressed in M. elongata grown in
culture than those sampled from the rhizosphere.
- Different genes are expressed in M. elongata inoculated on
different hosts.
Eddy Rubin
- Bacterial genes are typically ~900bp.
- In a couple of sequenced genomes they saw average
bacterial gene lengths as low as 200bp. However,
when they adjust the codon table by replacing one of the stop codons to code
for a glycine predicted genes have an average length of 900bp! Some bacteria use different codon
translations!
- Natalia Ivanova is a gene annotation specialist they
consulted for help in this analysis.
- They found evidence of recoding in lots of other bacteria
by looking at sequenced isolates.
- Didn’t find evidence of recoding in archea.
- They show that phages which use different codon profiles
can circumvent host cell machinery to match their codon profile!
- CRISPR regions in bacterial cells often contain phage
elements that correspond to different codon profiles. This is further evidence that phages with
different codon profiles can infect cells with canonical codon profiles.
Nicole Dublier
–Metagenomics and Metaproteomic Analyses of Symbioses between Bacteria and
Gutless Marine Worms
- Bacteria can use hydrogen to produce more energy than
methane. Nature 2011
- They discovered key genes able to metabolize hydrogen.
- The second half of the talk was about gutless worms living
in shallow water. They completely
dependent on bacterial symbionts for feeding and waste excretion.
- There are species specific symbionts.
- Her proteomics data yield more obvious features than
comparative genomics. As an example she
shows how one isolate contains a protein that does the function of 3 different
proteins in the canonical Calvin Cycle.
DNA sequencing confirmed this observation but would have been a
“needle-in-a-haystack” for a comparative genomics project. This work published in PNAS.
Erin Nuccio – Mapping
Soil Carbon from Cradle to Grave: Using
Omics and Isotope Analyses to Identify the Microbial Blueprint for
Root-enhanced Decomposition of Organic Matter.
- The general question is how do microbes transform and
stabilize root carbon in soil.
- Carbon can affect nitrogen rates.
- Plants fix carbon for microbes in the soil.
- Looking at the rhizosphere over time it gradually deviates
from bulk soil in carbon levels at time points of 3, 6, 9, and 12 weeks.
- Some preliminary data show that bacteria prefer carbon
excreted by plant over as an energy source over nitrogen liter material (ie
material artificially added to the system).
Michael Fischbach – A
Gene-to-Molecule Approach to the Discovery and Characterization of Natural
Products
- Discovers natural gene products. By gene products I think he means functional
protein units.
- Undiscovered gene products are often coded by clusters of
genes.
- Has some type of algorithm to computationally discover
these clusters that may produce unknown gene products.
- Lots of his most interesting clusters were found on human
associated microbes.
- Discovered several oligosaccharide clusters. These bacteria were very difficult to work
with but these clusters and the functions they provide to the human host are of
high interest.
- The general observation of this study was that microbes in
our gut are making products for which we have no idea what they are or how they
function. It’s like taking several
prescription drugs for your entire life!
We need to figure out what is going on in there.
Kelly Matzen –
Genetic Control of Mosquitoes
- In the 50’s DDT was used to control mosquito populations
and subsequently mosquito born disease such as dengue. However, DDT is know to be detrimental to the
environment in several ways and therefore is being used much less. We are starting to see diseases like dengue
make a comeback in places like Florida and of course in places like Central and
South America.
- Right now the most effective control is pesticides.
- They are releasing massive numbers of sterile male
mosquitoes to control (ie reduce) mosquito populations. This technique has been successfully used
before in the United States to control populations of other insects many years
ago.
- This technique seems to be working in the small field
studies they have been conducting.
- There is some push back from legislators but in general it
seems like good solution.
Cameron Coates –
Characterization of Cyanobacterial Hydrocarbon composition and Distribution of
Biosynthetic Pathways
- Cyanobacteria produce over 30% of the earth’s oxygen.
- They are very diverse and live in all sorts of habitats on
earth.
- They can produce hydrocarbons where are relevant of use of
biofuels. However, they don’t produce
large amounts of hydorcarbons.
- They looked at the evolution of cyanobacteria hydrocarbon
pathways. There are two main pathways. Several clades have both pathways suggesting
a large amount of horizontal gene transfer.
- This work was published in PLOS ONE.
June Medford – Making
Better Plants: Synthetic Approaches in
Plant Engineering
- They created a biological input/output system. This allows for some external factor to cause
a reaction that can be observed in the plant.
- They use a pariplasmic binding protein as the input signal
because it can quickly defuse through the cell wall and are then translocated
to the nucleus to transcriptionally regulate some response.
- They can theoretically use this system as a flag for
pollutants or other dangers that we currently use very expensive technology to
detect.
- They are currently developing a system to detect TNT where
the response signal of the plant is to turn white. This system can detect traces of TNT 10x
smaller than a dog! There are still some
kinks to work through like response time.
But looks like a very promising system.
This idea has countless unexplored applications!
Kankshita Swaminathan
– Genome Biology of Miscanthus
- Miscanthus is in the same clade as sugar cane, corn, and
sorghum. These plants have been amenable
to breading.
- The genomic sequence of sorghum is very close to
Miscanthus except that Miscanthus has had a whole genome duplication event.
- In the winter all the nutrients migrate to the rhizome
leaving only the stalk above ground. The
stalk is the most important element for biofuels and can be harvested without
significantly depleting soil nutrients.
Annalee Newitz (closing keynote) - How Humans Will Survive a Mass Extinction
- Humans have a very good chance of surviving a mass extinction because we are very adaptable. However, our focus should be how we can preserve the diversity of the earth as it is now.
- A mass extinction is when greater than 70% of the earth's species are killed.
- Five mass extinctions have occurred in the history of the earth. Perhaps the largest was caused by cyanobacteria because they released large amounts of oxygen into the atmosphere. Close to 90% of species became extinct as a result.
- Climate change is inevitable regardless of wither or not humans are the cause.
- The questions we should be asking are: how can we respond to these changing climates and what can we do to preserve the world as we know it.
- Space travel seems like an important step in human survival.
