Posts in category Education

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The Hill School: Day 2

The day started early Tuesday with first period.  Thirty eager students arrived on the bus to determine the results of the amplification of the DNA they extracted the day before.  The PCR ran overnight, copying part of a conserved gene in plants, RuBisCo, that can be used to identify the species of land plants.

Loading Gels at the Hill School

Loading Gels at the Hill School

 Using gel electrophoresis, we were able to load gels and run them quickly to see the results.  Most students successfully had amplicons – this was a great since they had not ever done DNA extraction or electrophoresis. The samples have been brought back to Rockville for sequencing and will be available for the students to analyze in about two-weeks.
Loading Gels like a Professional at the Hill School

Loading Gels like a Professional at the Hill School

We had a great visit with the students and are curious to see what plants they brought from around campus.

We look forward to working with them again in the future!

To support our Education program visit http://www.jcvi.org/cms/giving/overview

The Hill School: Day 1

DiscoverGenomics! Mobile Laboratory at the Hill School

DiscoverGenomics! Mobile Laboratory at the Hill School

The day started early with reagent and lab preparation before we even left for school OR had coffee.  We expected to do over 100 DNA Extractions as the first step in the DNA Barcoding. We arrived on campus as the first period was starting –we didn’t have class until after 9:00.

Grinding samples at the Hill School

Grinding samples at the Hill School

 It was a full house (bus) most of the day and busy getting through the DNA extraction.  Various specimens were brought in from around campus to determine their species.  It will be interesting to see the diversity of plants on campus.

Moving through the protocol at The Hill School

Moving through the protocol at The Hill SchoolThe Hill School

 

The Hill School

The Hill School

The Mobile Laboratory Hits the Road

After a hiatus this summer, the Mobile Laboratory hit the road again today for a trip to Pottstown, Pennsylvania.  Driving through the rolling hills of northern Maryland into southeastern Pennsylvania, it passed small towns and beautiful foliage.  Tomorrow and Tuesday, we will be working with students from the Hill School. 

The students will be exploring their campus by determining the species of plants they collect.  This process is often called “DNA Barcoding.”  DNA Barcoding is a standardized procedure using PCR, sequencing and bioinformatic analysis to determine the various species of plants, bacteria, etc. based on conserved genes.

Stay posted for more updates tomorrow!

A Look Back at 2010 at the JCVI…

As the J. Craig Venter Institute (JCVI) soars into its 19th year, we reflect on the past year of highlights and accomplishments to mark the close 2010 and look forward to more significant scientific advances in 2011.

JCVI Top 10 of 2010 …

1. First Synthetic Cell: Fifteen years in the making, 2010 brought to bear with huge anticipation the successful construction of the first self-replicating, synthetic bacterial cell. The work was published in Science in May. The synthetic cell called Mycoplasma mycoides JCVI-syn1.0 is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by an artificial genome. Although the first synthetic cell was not designed to produce a specific bioproduct, the team has shown that this can be done and the potential benefits are numerous. The research team, lead by JCVI President Craig Venter, Hamilton Smith, Clyde Hutchison, and Daniel Gibson, envision a future where the rapid design and production of biological products using synthetic biology techniques will be used to produce clean fuels, medicines, and other bioproducts. Throughout the course of this work, the JCVI Policy group has extensively engaged in outside review of the ethical and societal implications of this work, including advising the new Presidential Commission on Bioethics on their recommendations for oversight.

M. mycoides JCVI-syn1

M. mycoides JCVI-syn1

2. Synthetic Vaccines: Following on the heels of the announcement of the first synthetic cell, the company Synthetic Genomics Inc. and JCVI announced in October the formation of a new company, Synthetic Genomics Vaccines Inc. (SGVI). The privately held company is focused on developing next generation vaccines that can be rapidly produced and tested, which is especially important for outbreaks of new infectious diseases. SGVI also announced a three-year collaboration with Novartis to apply synthetic genomics technologies to accelerate the production of the influenza (flu) seed strains required for vaccine manufacturing. The seed strain is the starter culture of a virus, and is the base from which larger quantities of the vaccine virus can be grown. Under this collaboration, Novartis and SGVI will work to develop a “bank” of synthetically constructed seed viruses ready to go into production as soon as WHO makes recommendations on the flu strains. The technology could reduce vaccine production time by up to two months, which is particularly critical in the event of a pandemic.

3. Hydra Genome – one of the animal kingdom’s earliest common ancestors: JCVI scientists along with more than 70 other researchers from around the world, have sequenced and analyzed the genome of Hydra magnipapillata, a fresh water member of the cnidaria– stinging animals that include jellyfish, sea anemones and corals. The research, published in the March 14 edition of Nature, was co-led by Ewen F. Kirkness, JCVI, Jarrod A. Chapman, Department of Energy Joint Genome Institute, and Oleg Simakov, University of California, Berkeley. This is the second sequenced cnidarian genome, following that of a sea anemone, Nematostella vectensis, in 2007. The ancestors of these two species diverged more than 500 million years ago, and comparison of their genomes has revealed common features of the earliest animals that gave rise to the diversity of animals on Earth today. The team found clear evidence for conserved genome structure between the Hydra and other animals, like humans. Unexpectedly, the sequencing also revealed a novel bacterium that lives in close association with the Hydra.

4. Uncovering the Human Microbiome: Microbes are living within and on the human body and this collective community is called the human microbiome. JCVI Scientists, as one component of the large scale NIH Roadmap Human Microbiome Project, and along with colleagues at three other genome centers sequenced the genomes of ~180 microbes from the human body, published in the May 21 edition of Science. At the JCVI we anticipate sequencing an additional 400 species over the next few months. Colleagues at the JCVI are also using single cell approaches to isolate new strains that have not been cultured – isolates whose genomes will also be completely sequenced. The role these microbes play in human health and disease is still relatively unknown and these approaches are allowing us to gain a greater understanding of these enigmatic species.

5. Body Louse Genome: A global research team led by Ewen Kirkness and colleagues from JCVI published a study in the Proceedings of the National Academy of Sciences in June describing the sequencing and analysis of the human body louse, Pediculus humanus humanus, a human parasite responsible for the transmission of bacteria that cause epidemic typhus, relapsing fever and trench fever. Detailed analysis of the genome was then conducted by a large international group of 71 scientists, coordinated by Barry Pittendrigh, University of Illinois, and Professor Evgeny Zdobnov, University of Geneva Medical School. Comparative studies of the body louse genome with other species revealed features that will enhance our understanding of the relationships between disease-vector insects, the pathogens they transmit, and the human hosts. In addition to the targeted louse genome, the project unexpectedly yielded the complete genome sequence of a bacterial species, Riesia, that lives in close association with lice, and which is essential for survival of the insects. The researchers believe that the genome will be a valuable reference for evolutionary studies of insect species, especially in the areas related to insect growth and development.

6. Castor Bean Genome Sequencing: A research team co-led by Agnes P. Chan and colleagues from JCVI and Jonathan Crabtree and others at the Institute for Genome Sciences, University of Maryland School of Medicine, published the sequence and analysis of the castor bean (Ricinus communis) genome in Nature Biotechnology in August. Because of the potential use of castor bean as a biofuel and its production of the potent toxin ricin, the team focused efforts on analysis of genes related to oil and ricin production. The analyses could be important for comparative studies with other oilseed crops, and could also allow for genetic engineering of castor bean to produce oil without ricin. Identifying and understanding the ricin–producing gene family in castor bean will be important in preventing and dealing with potential bioterrorism events. Genomics enables enhanced diagnostic and forensic methods for the detection of ricin and precise identification of strains and geographical origins. As a next step, the group suggests further comparative genomic studies with the close relative cassava, a major crop in the developing world, to further elucidate their disease resistance aspects.

7. Science Education: JCVI was an Official Partner of the inaugural USA Science and Engineering Festival held on the National Mall in Washington, DC in October. The Festival, which was the country’s first national science festival, included over 500 of the country’s leading science and engineering organizations with the aim to reignite the interest of our nation’s youth in the sciences. The JCVI ‘Discover Genomes’ Bus was showcased during a two-day expo and some of the research being done at JCVI was presented to around 1700 visitors by our scientists and staff.

There were lines all day!

8. Viral Genomics– In 2010 the JCVI has published over 1600 influenza genomes and over 75% of all published flu genomes to date have been sequenced by the JCVI, totaling over 6000 genomes. This year the diversity of viral genomes we have sequenced has significantly expanded under the NIH Genomic Sequencing Center for Infectious Diseases contract. Some of the projects include viruses causing diseases such as measles, mumps, rubella, encephalitis, SARS, and the common cold, just to name a few. The viral group has annotated and published 79 Rotavirus (stomach flu) and 33 Coronavirus genomes (includes SARS and common cold) this year and many more will be published in 2011. The pace of sequencing and finishing genomes has also increased this year as a result of adoption of nextgen platforms (e.g. Illumina/454 and Illumina/Solexa) and the development of more efficient methodologies to increase productivity while reducing costs.

9. Marine Microbial Genome Sequencing Project: JCVI scientists have continued their quest to isolate and sequencing microbes living in global ocean waters to discover new genes and enzymes, and to help understand the role microbes play in the ocean ecosystem. Shibu Yooseph, Kenneth Nealson and colleagues at JCVI published an analysis of 137 known marine microbial genomes living in the global ocean surface in Nature in November. These genomes were compared to metagenomic samples of ocean waters of 10.97 million sequences of JCVI’s Sorcerer II Global Ocean Sampling (GOS) metagenomic data and thousands of 16S rRNA sequences. The marine genomes were collected as part of the Gordon and Betty Moore Foundation-funded Marine Microbial Genome Sequencing Project, a project coordinated by JCVI that has a primary goal of obtaining whole genome sequences of ecologically important microbes from a variety of diverse, global marine environments. The work provides a good example of combining metagenomic data with sequenced genomes data to study microbial communities and to generate testable hypotheses in microbial ecology.

10. Sorcerer II Global Ocean Sampling Expedition: On December 17th 2010 Sorcerer II arrived in Florida after spending the last two years with her crew collecting samples in The Baltic, Mediterranean and Black Seas. Funded generously by the Beyster Family Foundation Fund, The San Diego Foundation, and Life Technologies Foundation, Sorcerer II has sailed ~28,000 nautical miles since departing San Diego in March 2009. During this time 212 samples were collected and over 5,100 liters of sea water was filtered and sent to JCVI for analysis of the microbial life contained within these samples. The JCVI established strong collaborations with scientists in all 16 countries in which samples were collected, which will lead to joint publications and future collaborative studies in the new year. Read more.

Sunrise in the Ligurian Sea

Looking Forward to 2011…

Ten-year anniversary of the Human Genome Project: To commemorate the anniversary of the publications of the first human genome sequences in 2001, JCVI and Nature are hosting a conference and celebration in February 2011 titled – Human Genomics: The Next 10 Years. The conference will look forward to the promises of human genomics for the next 10 years, with sessions on medical advances related to genomics; the technological and ethical challenges of human genomics; personalized and familial genomics; the human microbiome project; variation in the human genome; and making sense of the genetic code. This conference will be a great way to jump into the new year and inspire the grandiose ideas and achievements that genomic scientists will accomplish over the years to come.

2011 Internship Program Updated

The 2011 JCVI Internship Program is open to accept spring and summer applications. The application process includes the submission of a resume, essay and transcripts as one PDF file via our online application site. We no longer require letters of recommendation.

Information about the 2011 program can be found at http://www.jcvi.org/cms/education/internship-program/

Hopefully this winter, we won’t be hit with two MAJOR snow storms in Maryland that shut all the schools, the federal government and JCVI down for several days the week applications were due! I don’t think they are calling for much snow this year in the Washington Metropolitan Area. Of course, that is not a problem for our colleagues in San Diego.

JCVI Rockville February 2010

JCVI Rockville February 2010

Some interesting facts about the summer internships from last year:

366 applicants applied online
44 Interns were selected:

8 high school students
19 undergraduate students
13 graduate students
4 secondary teachers

12 of the 44 were in San Diego and 32 in Rockville

The intern projects ranged across the Institute:

  • Shewanella oneidensis Growth in Chemostats
  • Purification and Characterization of a Pyrenoid Localized Decarboxylase
  • M. mycoides Minimalization: Combinatorial Assembly
  • Molecular Detection of Temperate Phages and Lysogens in the Marine Environment
  • Comparing the Performance of Short-Read Genome Assemblers
  • Phylogenetic Analysis of Cecal Microbiota in Alcohol-Induced Dysbacteriotic Mice, and Comparison of Pyrosequencing and Sanger Sequencing Technologies
  • Laboratory Research and Environmental Health & Safety (included making a safety video)
  • The Role of Accounting

Good luck to all the applicants this year!

USA Science & Engineering Festival

What a great weekend! Thousands of people attended the USA Science and Engineering Festival.  There were exhibits and performances for everyone, every age and every interest!

Open for business!

The DiscoverGenomics! Mobile Lab was there - Pennsylvania Avenue with several other mobile labs from across the country. We were just down the street from the Capital.

Looking down Pennsylvania Avenue - the Capital!

Building upon our previous exhibits, people were exposed to how genomics is being used to better understand the microbial diversity of our world at the Institute.  In addition, we looked at how microbes can be “put to work” via microbial fuel cells – even to facilitate the treatments of waste water.  Fascinating!!

Greg Wanger describing what is under the microscopes.

We started with exploring the amazing microbial world of the Rockville Campus storm pond.  Greg Wanger was the master at the scopes.  We had beatiful cyanobacteria from the green slime edge not to mention all the spirochettes and rod-shaped bacterium swimming by – even a few daphnia, worms and other organisms made an appearance as well!

From there, we learned how we can study these microorganisms from the enviroment through creating mini-eco systems with the pond mud.  Its amazing that there are so many unknown bacteria.  What are they doing?

We put them to work in the mud fuel cell.  Here – we could actually measure their power.  How do bacteria transfer electrons? What type are the most effecient? These are some basic questions we can answer with genomics.   

 Finally, we really put the bacteria to work with the waste water.  You may recall, Orianna Brestchger posted “Waste-to-Electricity” in January.  She wrapped up the exhibit with models of the fuel cell and data.

Orianna Brestchger discussing her project.

We had several JCVI staff helping Greg and Orianna: Crystal Snowden, Monica Thomas, Darryl Bronson, Jason Miller, Marcus Jones, Elaine Fox, Bea Gallogly, Matt LaPointe and Jasmine Pollard. 

There were lines all day!

Happy DNA Day!!

Happy DNA Day!!

This past March, we had a great time participating in the science programs in San Diego. We ended the month with the SD Science Festival with over 30,000 participants. It was such a busy day – I forgot to take pictures. The venue was Petco Park with hundreds of exhibits and hands-on experiences. We had our sediment batteries and microscopes.

With the thaw in Maryland from the multiple snow storms, April is beginning to show signs of spring including the Rockville Science Day. This will take place this Sunday, April 25 at Montgomery College, Rockville Campus. We should be easy to find – look for a big black bus.

In addition to the spring festivals and our school visits, behind the scenes we’ve been busy reviewing/selecting interns and setting up our summer professional development schedule. We had over 360 applicants this year to our internship program from all over the US and world. The blizzards this winter didn’t hold back the applicants. Notifications were be emailed to all on Friday, April 16th to the email address provided on the application. The applicants were so impressive!! Unfortunately we are not able to host everyone.

Our professional development programs were announced this month with support from Life Technologies Foundation. We are fortunate to be able to partner with such generous sponsors to bring these programs to fruition. We are REALLY excited about this year’s programs. They are filling up. California is almost FULL – be sure to send your application in. Maryland has room still – but don’t delay.

On that note, the Genomics Course for Educators on both coasts have biodiversity as the research theme. Our understanding of the diversity of life barely scratches the surfaces (literally). There are so many bacteria on and in our planet, not to mention our bodies – we are just beginning to know they exist – let alone, understand their significance. Even in our macro world, not every species has been catalogued! So much work to be done!!!

We are partnering with the Canadian Barcoding of Life Network with several other organizations in the MacArthur HASTAC Digital Media and Learning Competition. The project is to develop a fun science social networking site to encourage students to participate as citizen scientists and participate in developing a digital list of all organisms around the country and world. Please review the video at the link below and provide comments. It is important that the comments are added via the HSTAC site – the YouTube comments do not carry over. These comments are used in the decision making for funding.

http://www.dmlcompetition.net/pligg/story.php?title=400

Thanks for your support!!!

And, again, Happy DNA Day!!!

A Positive Charge

I’m thinking of the day’s schedule school visit, the activity and the positive charge it will produce in me and the students.  I get so excited during our school visits.  It’s like the feeling I get on Saturday morning while watching my favorite cartoons. (Yes, I still watch cartoons)  The first class I ever taught was at Hine Jr. High School in Washington D.C. in 2005 and the activity was Mystery of the Crooked Cell. 

After the classroom visits,  the Science Fairs, After School Programs, NIST Adventure in Science and Take Your Child to Work Day programs, in this my 5th year as Mobile Lab Driver and Teaching Assistant, I still get excited when working with a group of students.  I’m the preverbal kid in a candy store with the keys and I even make the candy!

 As I ponder this, another thought comes to mind, in our effort to reinforce specific standards of science and exposure to FUN!  I have come to understand the importance of the program and the positive charge on students, teachers and the community.  In a time of educational cut backs, the layoff of teachers and the closing of schools, the DiscoverGenomic! Science Education Program is a sure sign that we have not left any child behind.

Thanks for a positive charge DG! Science Education Program!

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!!

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.