Monthly Archive for March, 2010

We Had Fun with Genomics!!

BEWiSE March 6 & 13 at JCVI

BEWiSE March 6 & 13 at JCVI

Wow! It’s been an exciting week!! Crystal Snowden and I flew to San Diego Friday, March 5th – jumped off the plane and the fun began!  We went straight to the lab and set up for BEWiSE and prepped for Expanding Your Horizons (EYH).  We are really fortunate to have such a great team in the San Diego facility.

Saturday started early with Crystal Snowden heading out to EYH at University of San Diego.  I did not go, but Crystal said it was an AWESOME time.  She worked with 45 young ladies.  The students learned about Winograsky columns and how the environmental organisms contributed to the microbial fuel cells and waste water treatment.  They prepared microscope slides by staining bacteria and viewed them under the microscopes.  The participants ranged in age from 12 to 16.  Unfortunately, Crystal was too busy to take pictures!  The quote of the day was, “This is AWESOME!”

Pipetting in the lab

Pipetting in the lab

While Crystal was busy at USD, Orianna Bretschger, Shino Ishii, Angela Wu, Eric Son and I hosted 16 young ladies from BEWiSE. Our day started early too at 9:00, running through 2:30.  We learned about genomics, microbial fuel cells and waste water treatment.  In the labs, the girls mastered pipetting and DNA extraction culminating with DNA isolation from the Winograsky columns.  The day ended with setting up PCR of the DNA isolates.  It was like riding a lab train.

Orianna Bretschger is helping get the mud samples - stinky!!

Orianna Bretschger is helping get the mud samples - stinky!!

During the week, Crystal finished the students’ samples through library construction and the second PCR.  The samples then traveled east to Rockville for sequencing, where Monica Thomas picked up the process.  She prepped them for sequencing and came in at 3:00AM Saturday morning to pull the data off the sequencers for us.  Wow! That is team work AND dedication.

We started again Saturday, March 13th early at 9:00AM.  I knew the samples worked, but the BEWiSE participants didn’t.  We poured our agarose gels, used a new buffer that enables the gels to run faster, checked out the transformation plates – ending with a BLAST search of their sequence DATA.    Of the eight groups, six had data – the sequencing of the 16s RNA gene matched uncultured bacteria.  Cool!  Some were related to Cyanobacteria – even cooler!  It was a great time for young ladies and JCVI staff.  We get invigorated too!!!

How could the week get better? In the middle of the week, we also exhibited at the San Diego Science Alliance High Tech Fair as I noted in my last posting.  We brought the Winograsky columns, the sediment tanks and the microscopes.  We recruited a few more JCVI staff and scientists to help – Sue Fields, Greg Wanger, Jeff McLean, Adi Ramon and Jeff McQuaid.  Under the scopes we had some estuary water with algae, small bacteria and paramecium – cool.  For our younger guests, we also had Daphnia to look at.  With the scopes, we were able to draw participants’ interest and then talk about our batteries and water reclamation.  Tuesday night, we had participants of all ages – 800 in two-hours.  Wednesday, there were at least 1,000 students being bus’d in from all over San Diego.  The booth was rockin’ and rollin’ – and it wasn’t just because the booth next to us had Guitar Hero™.
Orianna Brestchger at the SDSA High Tech Fair!

Orianna Bretschger at the SDSA High Tech Fair!

I flew back to Maryland Sunday – exhausted.  It was a GREAT week!  I hope to see all the BEWiSE girls applying for internships in the next year or two.  Don’t forget to tell your teachers what you did!

For more pictures – visit our Facebook page.

Watch for us at the SD Science Festival on MARCH 27th!!

Scientist Spotlight: Orianna Bretschger

Most of us have never thought about how to make more water or cleaner water or develop unique sources of energy but that’s exactly what Orianna Bretschger does at JCVI.  She is working at the intersection of engineering, physics, and biology to design small machines powered by bacteria that can purify wastewater and generate electricity at the same time.

Orianna Bretschger

Orianna Bretschger

Working in alternative energy was a natural career choice for Orianna since she grew up in the desert in Arizona where water was a precious and finite commodity. She also lived in places without electricity or plumbing.  One place, that holds fond memories for her, had an old-fashioned windmill that was used to pump water into an open tank for cattle.

Orianna always had an interest in science, especially astronomy, and with that interest, coupled to good teachers who always inspired her, she found her way to where she is now.

At an early age, Orianna entered the Young Astronauts program.  She had been introduced to the program by the school director, who happened to be a nun, who was at one time on the short list for the “teacher in space program.”  By junior high Orianna had attended two International Young Astronauts conferences, toured the Johnson and Kennedy Space Centers, and travelled to the former USSR with her mentors and another student to help build relationships with Young Kosmonauts; a trip that solidified her love of science.

In high school she expanded her science interests to physics and planetary science, and had the opportunity to present a poster at a Lunar and Planetary Science conference at the Johnson Space Center in Houston.  Incidentally, her teacher for these courses was also her cross-country coach – he encouraged her to go to school at Northern Arizona University, in Flagstaff, AZ (where the “dwarf planet” Pluto was discovered) where she earned a merged degree in physics and astronomy.

After her undergraduate education, Orianna went into industry, landing a job at Raytheon Missile Systems in Tucson, Arizona. There she worked on guidance systems, supporting projects in the Electro-optical subsystems department for two years, something she considers to be a great experience.  As part of her work there on the Algorithm and Analysis team she developed algorithms for the guidance systems and began the efforts to test and validate the system. As part of her job she got to fly in old military planes, collecting and analyzing flight data and system performance.

At the end of two years at Raytheon, she still had not made the decision to attend graduate school but instead headed to Authenti-Corp, a company that is involved in biometrics evaluation (e.g. facial and voice recognition devices, fingerprint and iris scanners, digital signature verification, smart cards etc.)  where her primary job was working with the Department of the Army Biometrics Task Force to develop policies and procedures for biometric systems testing and implementation. She decided that government contracting was not for her, and subsequently worked various jobs for a couple of years, including bartending in her time off, to prepare for grad school.

Orianna decided on University of Southern California, where she was accepted into the Materials Science Ph.D. program in the School of Engineering. She spent her first semester working in a Carbon Composites lab, and later met Ken Nealson in the Biology Department where she began working on microbial fuel cells (MFCs) in Ken’s laboratory.   Graduate work was focused on identifying the specific genes in the organism Shewanella oneidensis MR-1 involved with electrical current production, and solid-phase manganese and iron oxide reduction. She also led the effort to characterize the power performance, fuel flexibility, and metabolic activity of several other Shewanella wild-type strains and environmental enrichments. Throughout these projects she was given the opportunity to learn and practice microbial physiology, reactor design, electrochemistry, analytical chemistry, and environmental engineering.  She graduated in the summer of 2008 and then joined JCVI with Ken.

Orianna really enjoys the diversity of science at JCVI and according to her the wonderful people make for a terrific work environment. Specifically her interests are to extend the technology for sustainable wastewater treatment, energy recovery, and develop MFC systems for the study of microbial physiology.  Ten years from now she hopes to be tenured faculty, and believes her work with engineered and biological systems will ultimately contribute to developing healthy and sustainable water management practices throughout the Southwest and worldwide.

Note: Adapted from the original article written by Karen Nelson, Director of JCVI’s Rockville campus.

Having Fun with Genomics

I am the generation after landing on the moon. As a child, I don’t recall having any science inspiration. I was fortunate to have parents that made it possible for me and my siblings to get a very good education. I went to a small parochial school outside of Washington, DC. It was a great school but we had no labs and so my exposure to science was limited at best.  I always liked school and did well, especially in math.

Then I went to Elizabeth Seton High School and had a bumpy road of it. I had two strong teachers mentoring me, Sr. Lani, my homeroom teacher, and Sr. Mary Marguerite in Pre Calculus and Calculus. Though I still had no real strong interest in science, I decided to take AP Biology in senior year. Ms. D’Apolito made us read science journals. Wow! That was unbelievably hard!! I struggled. But in this class, Ms. D’Apolito brought her love of science and research experience into the classroom. I vividly remember reading a journal article about E. coli and thought, “This is so cool! I want to go into research.” And my friends thought I was crazy. So off to college I went, majoring in nursing.

Staying locally, I entered the Catholic University of America, planning to concentrate in nursing. My first year chemistry was taught by this incredible teacher, Dr. Diane Bunce, who is currently a Nifty Fifty with the USA Science and Engineering Festival. She made chemistry exciting and alive!! My second semester, I knew I really wanted to study science. Through many discussions with Dr. Bunce, I realized with a chemistry degree I could do anything from make new plastics to make new cosmetics (her sister worked at a major cosmetic company). Finally, I decided I really wanted Biochemistry – I love photosynthesis!! From there, I continued to work with Dr. Bunce who specialized in chemistry education. I was a teaching assistant (TA) for her professional development in the summer – working with high school chemistry teachers – and I TA’d in her non-science major chemistry class. Dr. Bunce is one of my greatest mentors.

From there, I graduated and had another extraordinary opportunity to come to work in what was described as a “controversial” lab at NIH. I had no idea what I was walking into – but am extremely grateful that Dr. Venter gave me the opportunity to work in his lab. From there, you can read Dr. Venter’s book. I participated in the greatest scientific revolution – the beginnings of genomics!! Furthermore, I have gotten back to my roots – I get to work with teachers, students and “non-science” community to excite them about science and genomics.

Why do I share my story? To explain the difference between my school science experience and the opportunities that exists today for kids of all ages. I never had the opportunity to participate in science enrichment programs because very few existed then. This coming week, JCVI is presenting at two awesome events and hosting a group of young women for a special program in San Diego. First, March 6 and 13, we will be hosting BEWiSE, Better Education for Women in Science & Engineering. BEWiSE is a program of the San Diego Science Alliance and makes a difference for talented young women who are encouraged to contribute to science and engineering professions. Twenty 9th graders will have the opportunity to explore the microbial diversity from soil in a sediment battery by working with JCVI’s Orianna Bretschger. Wow! I never did this in high school or college.

We are also presenting on March 6th at the “Expanding Your Horizon Conference” at the University of San Diego. My colleague, Crystal Snowden, will be hosting a workshop discussing the sediment fuel cell and exploring the bacteria present. This conference reaches out to young girls too! What fun to see the critters under the microscope!

Finally, we will be exhibiting along with several other organizations in the area at the San Diego Science Alliance High Tech Fair. Here, we will have the sediment batteries, microscopes for viewing sea water microbes and soil bacteria, plus slides of diatoms found in Antarctica. Did you really think that electricity could be generated from mud, let alone, sludge??

I wish I had the opportunity to go to programs like this when I was young! You never know when that spark will be lit – in a classroom, at a science festival, watching the waves or a discussion over dinner. Finally, a big thank you goes to all my mentors I’ve had in my life: Sr. Lani, Sr. Mary Marguerite, Ms. D’Apolito, Dr. Bunce and Dr. Venter!

Have you thanked your teachers and mentors lately?

Watch for pictures next week.

AGBT, Marco Island 2010

I just got back from AGBT in Marco Island, Florida and I am still in awe. As noted in the name, this conference highlights advances in both genome biology and technology.  The biology seemed to be very human genome centric.  Many of the talks presented full genome sequences of cancer genomes or familial cohorts.  Some of the numbers that people threw around were shocking. It was only a short time ago that Craig Venter came out with the first personal genome, and now sequencing centers like Washington University in St. Louis and the Broad are talking about sequencing hundreds of human genomes in a year.  I was really impressed by a talk from Wash-U where they sequenced 4 exomes for Miller’s syndrome – two normal parents and two affected children – and discovered the causative gene.  They were also very honest about their efforts not being as readily successful in a variety of other Mendelian autosomal recessive traits.

One of the more interesting fallouts from all this sequencing is that everyone is submitting to dbSNP; I think that soon nearly every base will have a SNP.  Unfortunately people are currently using dbSNP to filter out candidate SNPs for their study.  Their logic runs something like, “If it’s in dbSNP then it must be benign.”  You can easily see that with the sequencing of several hundred cancer genomes, this proposition will no longer hold.  dbSNP will hold a vast array of deleterious SNPs.  What it needs to transform into is not just a database of ‘Chr17:2345656 A->T’, but rather something that keeps track of frequency and phenotype. Also there was a discussion about false-discovery rates, and how to keep databases clean.  Some of these studies were going to submit 18 million new SNPs, with a 10% FDR. That’s 2 million false positives :(

The technology portion of the conference was amazing.  There were new instruments being rolled out by numerous companies, and they were all promising. I loved sitting and listening to the clever new set-ups. There were several single molecule sequencers which I am very excited for – because we can hopefully get past metagenomic pools and on to metagenomic genomes.

I was lucky to be chosen as a presenter in the Genome Informatics session on Thursday evening.  There were lots of talks about RNA-seq and getting more out of your sequencing data.  So I felt like a bit of an outsider not talking about sequencing.  My presentation was on proteogenomics, which uses proteomic data to improve genome annotation.  Then major thrust for this audience is that genome annotation is far from perfect, and proteomics evidence can reveal many novel proteins in every genome that I’ve come across. I think that as biology expands past E. coli and B. subtilis into the vastness of genome diversity, we are seeing genes that look nothing like we’ve ever imagined.  Rather, as I point out in the talk, we are often NOT seeing these new genes because gene predictors fail to recognize them.  I’ve attached the slides to the post for your viewing pleasure (Payne.AGBT.2010).  Let me know what you think.

Sam

Influenza H1N1pdm sequencing project overview

Since 2004, the JCVI Influenza Genome Sequencing Project, funded by the National Institute of Allergy and Infectious Diseases (NIAID), has sequenced thousands of human, swine, and avian influenza isolates from collections around the world to provide researchers with a better understanding of the evolution of this important pathogen and to enable the development of new therapeutics, diagnostics, and vaccines.

JCVI has been collaborating with groups worldwide to monitor the evolution of the pandemic H1N1 Influenza virus (also known as H1N1pdm) that entered the human population in the spring of 2009 and has been responsible for at least 16,226 deaths worldwide. Genomic sequence information and epidemiological data are being used to address critical scientific questions of virus adaptation.

Some of the questions we are trying to answer with our current H1N1pdm studies include:

  • How do pandemic viruses collected during the first wave of the pandemic compare to those collected in the later phases? We have ongoing studies in New York, Texas, Wisconsin, and California which address this question.
  • How will the presence of a new pandemic influenza virus affect the evolution of seasonal H1N1 and H3N2 viruses? Will the seasonal viruses become extinct? Will we identify novel reassortants between the H1N1pdm and seasonal human viruses?
  • Will the pandemic virus acquire resistance to neuraminidase inhibitors such as Tamiflu?
  • How does H1N1pdm isolated in the tropics differ from isolates collected in temperate regions? What is the relationship between strains present in the tropics and epidemic strains in temperate regions? We have collections in Nicaragua, Hong Kong, and Brazil which will help answer these questions.
  • What are the evolutionary dynamics of H1N1pdm in a situation of intense viral transmission such as between students in a university setting?
  • Influenza samples have never been collected during the summer months. Thus the collection of pandemic influenza samples during the summer gives us a glimpse of viral persistence and transmission during the off peak months. How do circulating influenza strains collected during the southern hemisphere’s influenza season compare to those collected during the US summer and which strains persist into the next northern hemisphere flu season?

For more information please visit http://gsc.jcvi.org/projects/msc/influenza/