Monthly Archive for July, 2011

What Happened to Sorcerer II?!?!

The last time I wrote a Sorcerer II blog was in November when we set sail from Spain to cross the Atlantic Ocean.  For all of you that have been worried that we have been at sea for 8 months, relax we made it!!  Over the next few days I will update everyone on what has happened and the upcoming plans for Sorcerer II.

First off, the Atlantic Crossing……….On November 13th we left Gibraltar and on November 17th arrived in the Canary Islands.

Canary Islands

Lanzarote Island

After a day on Lanzarote Island we sailed overnight to Las Palmas on Gran Canary, collecting two samples on the way.  We stayed in Las Palmas waiting for a good weather window for the big crossing.  During that time we traded out crew members, fully stocked the boat with food, supplies and fuel.  We also had time to meet our collaborators from the University of Las Palmas.  I gave a group from the University a tour of the boat and showed them the sampling equipment.

Giving a demo of the sample gear

Folks from University of Las Palmas

On November 22nd we took off for the USA USA USA!  There was one problem, a huge storm in the Northern Atlantic.  To avoid the storm we had to go much more south then originally planned, also this storm sucked all the wind up north, so we had very little wind to sail with.  With no wind and a much longer sail than planned, we couldn’t make it directly to Florida…………well we could have but we would have run out of fuel and food!  So on December 8th we arrived in St. Thomas USVI.  For two and a half weeks we motored our way from the Canary Islands to the USVI sampling and fishing.  Total fish count was 8 Mahi Mahi, 3 Wahoo and 2 Yellow Fin Tuna.

Route, Canary Islands to USVI

Les and Me with the catch of the day

Atlantic Ocean Sunset

John BBQ'ing dinner at sea

Crew Sampling

One more thing, during this crossing the following things all happened, the strange part is they all happened within 24 hours of each other!

1.  Little generator broke (not a big deal we have 2 generators), both were up and running in a few hours

2.  Auto-pilot went out……….could have been  a real pain  because we would have  had to hand steer 24 hours a day for the rest of the trip, this was on day 8, but it got fixed in a few hours as well.

3.  Water maker went down………no water for showers, dishes and oh yeah no drinking water……once again got fixed in a few hours

4.  Mainsail ripped, this was fixed a few days later, but for  those days we were pretty rolly out there with no mainsail to keep us steady.

5.  Busted pipe in my head (bathroom)………funny thing is I woke up around 4 am dreaming about waves then I woke up and still heard the waves; it was the water going back and forth in my bathroom floor!

6.  And the big daddy of them all…….. a full out engine room fire!!  Not just smoke or steam…….we are talking flames and extinguishers!  It was taken care of and the engine was up and running about 4 hours later.

On December 20th 2010 Sorcerer II arrived in Florida.  This wrapped up the 2009/2010 Europe Expedition.  During this time we collected 213 samples, filtered over 51,000 liters of water from 13 countries.  DNA from all 3 size fractions from the 213 samples have been extracted, although not all will be sequenced right away, a majority have been sequenced or are schedule to be sequenced this year.  I will write a future blog on the sequencing status of these 213 samples and how we are working with many collaborators from Europe to work up this data set.  I will also write about what has been going on with Sorcerer II since December 2010 and future plans for her.

Podcast on Human Genomics

The 2011 Festival of Ideas themed, The Pursuit of Identity, Landscape, History, and Genetics, is held every other year in Melbourne, Australia to inspire scholars and citizens alike in topics ranging from literature and art to science and foreign policy.  JCVI Professor of Genomic Medicine, Vanessa Hayes participated as a speaker at the festival, and was interviewed for podcast on “Out of Africa: What human genomics is revealing about us.”  The podcast and transcript provide an excellent discussion of modern genomics for a non-technical audience, including a glimpse of the exciting directions in the field and implications for human health.

A video of the session Vanessa Hayes participated in:  The Genetic Revolution I: Health and Human Identity can be downloaded here.

Summit on Systems Biology, June 15-17, 2011

I attended the Summit on Systems Biology hosted by Virginia Commonwealth University in Richmond, VA June 15-17.  So, judging from the talks given, what is systems biology?

  • Systems biology is non-linear and/or multi-step.  Heavy math does not make something systems biology if it’s directly solvable.  Taking a big gene expression matrix, using principle component analysis on it, and coming up with a linear equation for the contributions of a list of biomarker genes, is not systems biology.  The same microarray expression experiment, coupled with pathway analysis in order to reduce candidate genes and so do a less stringent multiple-hypothesis-testing-correction and so have fewer false negatives, is.  So is a non-linear model of how just a few genes interact over time.
  • Standard bioinformatic analysis seeks correlations.  Systems biology goes beyond that to seek cause and effect.  Thus, most systems biology work involves time series, and sometimes simulation.

What data and techniques do systems biologists use?

  • Large datasets of all types.  Microarray time-series, genomes, SNPs, protein-protein interactions, automated protein annotation – anything that comes in gigabytes instead of kilobytes.
  • There was marked interest in protein-protein interaction networks, and in micro RNAs (which inhibit translation of multiple target mRNAs).
  • There were several papers using reverse-phase protein microarrays.  RPMAs can distinguish phosphorylated (which usually means active) from unphosphorylated proteins, which helps understand protein interaction dynamics.
  • There were several papers using weighted gene co-expression network analysis.  WGCNA analyzes modules of co-expressed genes, rather than individual genes.  This gives more statistical power from sparse data.  Brian Sayre of VSU identified disease-resistance genes in livestock and crop species using single-nucleotide polymorphisms (SNPs) from related species.  We might know about some goats that are resistant to a disease that also affects sheep; but sheep don’t have the same SNPs as goats.  His group categorized the SNPs into genes, and the genes into pathways common across species, then looked for pathways associated with disease resistance in other species, and hypothesized that the same pathways would be involved in disease resistance in the target species.

What do people do with systems biology?

  • Medical applications predominated.  The main areas of interest were cancer, aging, cell simulation, eukaryotic model organisms, genome-wide association studies, pathway analysis, and immunology.
  • There were no talks about industrial applications or synthetic biology.
  • There were no talks on prokaryotes, except one on host-pathogen interactions.  This struck me as odd, since eukaryotes are more difficult to analyze or simulate than prokaryotes, and we haven’t done these things with prokaryotes yet.
  • There were no talks on metagenomics.  This also struck me as odd; bacterial communities seem like a natural systems biology problem.

What does the future hold for systems biology?

  • Omniomics:  We don’t want just a protein’s sequence – we want to know where and when it is expressed, what regulates it, what it interacts with, and what parameters describe those interactions. Soon, annotating a genome will not mean producing a list of genes and their functions – it will mean producing a simulation.
  • We need to learn to think at a higher level of abstraction.  If you have tens or hundreds of thousands of genes, transcripts, proteins, small molecules, and structures interacting, you need to figure out what it is you’re really interested in (e.g., “How did this cancer bypass the G1 cell-cycle restriction checkpoint?”), how to specify that precisely enough to ask the computer for an answer, and not to insist on understanding all the details if the answer checks out.
  • There is a growing gap between research and practice.  We can make more and more detailed analyses of diseases, especially in cancer, where each patient has a unique disease at the genetic level.  Meanwhile, the FDA approval process is so long and expensive that even in diseases (for example, Alzheimer’s and FTLD) for which there are millions of patients and a handful of known causes, pharmaceutical companies don’t try to develop three to four separate therapies for those three to four causes.  And the gap is growing wider:  Even as we are coming up with ways to combine weak information from across an entire genome, the FDA is considering proposals to regulate genomic sequencing that would forbid doctors from acquiring a full sequence.