Posts by JCVI Staff

Scientist Spotlight: Meet Sarah Highlander

Sarah Highlander Ph.D. is an esteemed scientist and professor who joined JCVI in La Jolla this year. She comes from a long line of academically successful Professors, including a great uncle who was a University Dean. As a young child, Sarah was influenced by her parents: her mother was a musician and her father was a Ph.D. chemical engineer. Sarah too was a musician and she still enjoys jazz and the opera. But it was her father’s scientific career that influenced her own decision to pursue scientific research as her career.

Dr. Sarah Highlander

Dr. Sarah Highlander

As a chemical engineer and early IT specialist, he shared his interests with her at the kitchen table by doing mathematical puzzles and simple experiments. They explored the impact light had on grass growth by placing plants in the closet. Then in high school, she had the opportunity to work on a microbiology project with the help of her father. Using agar slants from his colleague’s lab, she looked for antimicrobial features of bacteria in the soil. Even with these opportunities, her focus in the sciences wasn’t fully set until she began working as a technician in a fermentation research lab where she had the opportunity to work with plasmids after completing her bachelor’s degree. At this point, plasmids and restriction enzymes were not readily available and researchers had to isolate them in their labs. She was extremely successful as a technician and even published several papers and secured several patents.

This experience launched Highlander into Medical Microbiology. She went to the Sackler Institute of Biomedical Sciences at the New York University School of Medicine, where she earned her Ph.D. in 1985. With her curious nature and the bourgeoning field of biotechnology, she began to research the replication of DNA plasmids in Staphylococcus. She asked basic but as yet unanswered questions such as, “How are these molecules controlled in the cell?” and “How can they best be manipulated in the laboratory?” Her thesis involved characterizing small RNA molecules that control plasmid copy number.

During her Post-doctoral fellowship, she shifted her focus to infectious diseases and worked on vaccine development for a cattle disease called “shipping fever” at the University of Texas Health Science Center. Shipping fever is the most common and costly problem affecting calves. It accounts for major economic losses to the cattle producer by reducing average daily weight gain, impairs feed efficiency, and diminishes overall performance and health of beef calves. Vaccination is key to reduce the disease and Highlander’s research culminated in the development of a subunit vaccine that is still in use.

After her fellowship, she began her professorship at Baylor’s College of Medicine (BCM), where she continued her research into shipping fever. The primary bacterial agent in this disease is Mannheimia haemolytica, which is the same family as the human respiratory pathogen, Haemophilus influenzae. JCVI scientists were the first to sequence and publish the H flu genome in 1995. Dr. Highlander’s group performed extensive characterization of the M. haemolytica leukotoxin and developed numerous genetic tools for manipulation and tagging of the organism. She holds patents for subunit and live-attenuated vaccines to prevent shipping fever.

In 2002, Highlander founded Prokaryon Technologies, a for-profit company focused on animal health to prevent and control diseases associated with food animals. One of Prokaryon’s lead products was a genomics-derived vaccine to prevent shipping fever in cattle.

While leading and growing her company, Highlander stayed committed to her academic research interests and joined the Human Genome Sequencing Center at Baylor. At BCM, she participated in genome sequencing of several pathogens (including M. haemolytica) and she moved to focus more on human pathogens. From 2006 to 2013, Highlander was a principal investigator for the Human Microbiome Project (HMP), a National Institutes of Health-funded program in which JCVI researchers were also key leaders.

In addition to her research, Highlander was involved in graduate and medical education at BCM. She was the co-director of the departmental graduate program for 15 years and directed and taught courses focused on bacterial physiology and molecular laboratory methods. Preparation for lectures and interactions with students helped her stay on top of new techniques and research, which in turn helped her further her own research. Sarah had the opportunity to mentor many graduate students both formally and informally.

At JCVI, Highlander is continuing her work on the microbes that live in and on the human body. Specifically she and her team are looking at the complex microbial communities that live in the human gut. While many microbes are associated with disease, most in the human body are associated with health. Highlander and her team are working to develop specific healthy bacterial mixtures that could be used treat conditions such recurrent Clostridium difficile diarrhea, inflammatory bowel disease and others. She is also using bioinformatics tools to look for new causes of diarrhea. “I am delighted to be a part of the collaborative environment here at JCVI and to be surrounded by colleagues who share common interests in bacterial genetics, genomics, microbial physiology and pathogenesis. The microbiome group at JCVI is strong and I hope to be able to make significant contributions to ongoing and future projects here”.

Even in her personal life, Sarah researches, through her hobby of tracing her genealogy. She has been able to find family roots dating back to the 1500s. This detective work is challenging but it keeps her mind sharp and detailed oriented. She points out that learning family naming patterns can be critical to genealogy research just as algorithm development is to genomic research.

Never having lost that early scientific curiosity and excitement of discovery that her father instilled in her as a young girl, Sarah loves working in the laboratory at JCVI and asking questions. Her analytical and inquisitive nature is one of her greatest professional strengths. She is fascinated by the complexity of the microbial ecosystem in our bodies and the impact these microbes have on our health. As she says, “Microbes are going to continue to win through evolution. We need to figure out the next step to keep ahead!” Let’s hope Highlander and her team can win this battle.

JCVI Hosts South African Scientists to Share Microbiome Research Techniques

Two scientists from the University of Cape Town, South Africa have joined Dr. Bill Nierman’s lab for the next month as part of NIH’s Human Heredity and Health in Africa (H3Africa) Initiative, a training program designed to build out technical biological skills in the African research community. This training relates specifically to developing techniques around the area of microbiome analysis, a relatively new field in the biological sciences.

Microbiome analysis for the collaborative study is looking at entire community of microorganisms in the respiratory tract of South African infants to better understand how the microbiome is associated with infant pneumonia and wheezing episodes. The expectation is that the organisms that reside in the infant respiratory tract will provide protection from or a predisposition to the pneumonia or wheezing episodes.

 

The Nierman Group

The Nierman group left to right Sarah Lucas, Bill Nierman, Shantelle Claassen, Mamadou Kaba and Stephanie Mounaud (unpictured Jyoti Shanker and Lilliana Losada) welcomes visiting scientists Ms. Classeen and Dr. Kaba from University of Cape Town for a month long training in microbiome sequencing and analysis.

Mamado Kaba, MD, PhD and colleague Shantelle Claassen from the University of Cape Town will be working closely under the guidance of JCVI’s Stephanie Mounaud who is functioning as the project manager and coordinating the laboratory components of a similar project at JCVI studying the microbiomes of inafnts in the Philippines and also in South Africa. These studies are sponsored by the Bill and Melinda Gates Foundation. The training will focus initially on preparing samples for DNA sequencing on a modern DNA sequencing platform, the Illumina MiSeq instrument. Once the sequence reads are off the sequencer, the instructional focus will shift to analysis of the reads by means of an informatics pipeline that develop phylogenies, or family trees, of the microbes that are obtained from the infant respiratory tract so that the abundance and relatedness of the microbes can be established. The bioinformatics training will be provided by Jyoti Shankar, the statistical analyst working on the Gates Foundation Project.

Mamadou Kaba is a Wellcome Trust Fellow working in the Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town. Mamadou’s research interests include the molecular epidemiology of infectious diseases and the study of human microbiome in healthy and disease conditions. He has contributed in establishing a new research group conducting studies on how the composition of the upper respiratory tract, gastrointestinal, and the house dust microbial communities influences the development of respiratory diseases.

Prior to joining the University of Cape Town, Mamadou worked as Research Associate at the Laboratory of Medical Microbiology, Timone University Hospital, Marseille, France, where he studied the epidemiological characteristics of infection with hepatitis E virus in South-eastern France.

Shantelle Claassen is pursuing a Masters degree in the Division of Medical Microbiology at the University of Cape Town. She has completed a BSc (Med) Honours degree in Infectious Diseases and Immunology at the University of Cape Town, during which she examined the relative efficacy of extracting bacterial genomic DNA from human faecal samples using five commercial DNA extraction kits. The DNA extraction kits were evaluated based on their ability to efficiently lyse bacterial cells, cause minimal DNA shearing, produce reproducible results and ensure broad-range representation of bacterial diversity.

Mamadou and Shantelle are currently involved in an additional prospective, longitudinal study of which the primary objective is to investigate the association between fecal bacterial communities and recurrent wheezing during the first two years of life.

Building the World’s First Net-Zero Energy Lab [video]

Building the World’s First Net-Zero Energy Lab

And see the construction in time-lapes.

Amazon Expedition

Yesterday, JCVI expedition scientist Jeff Hoffman embarked from Manaus on a sampling expedition of the Amazon River and its tributaries, which contains 1/5th of the Earth’s river flow. In collaboration with scientists Dr. Guilherme Oliviera and Dr. Sara Cuadros from the Centro de Excelencia em Bioinformatica (CEBIO) of Belo Horizonte, Jeff is taking samples to characterize the genomes of microbes found along 2/3rds of the entire Amazon watershed, including inflowing rivers from Manaus to Macapa. Our collaborators at CEBIO will be sequencing the samples with a joint Brazil-USA effort on analysis. Long recognized for the biodiversity of visible organisms, the Amazon is understudied with regards to the diversity of microscopic organisms and this expedition will substantially increase our understanding of the biological diversity on Earth. This work continues, leverages, and complements previous and ongoing JCVI work characterizing the unexplored microbiomes of marine, estuarine, freshwater, and terrestrial environments around the world.

See a gallery of the expedition on Facebook. More pictures will be added throughout the trip.

Carl Woese 1928-2012

Editor’s Note: This post originally appeared on T. Taxus, December 31, 2012, by Jonathan Badger. Dr. Badger  is an Assistant Professor in the Microbial and Environmental Genomics Group at the J. Craig Venter Institute in La Jolla, CA. Reprinted by permission.

As you may have heard, Carl Woese died of pancreatic cancer yesterday at the age of 84. I had the honor of working with Carl in grad school at the University of Illinois where my advisor, Gary Olsen, ran a joint lab with Carl.

Carl Woese

Carl Woese. Photo courtesy IGB.

As the originator of the use of ribosomal RNA to distinguish and classify organisms (including obviously the Archaea), Carl both revolutionized evolutionary biology and created a method that is still very much in use today. Even in the latest metagenomic study of the oceans or of the human gut, a 16S rRNA diversity study is required as a control in addition to whatever additional markers or random sequencing is used.

One of the things that fascinated me about Carl is how he constantly reinvented himself and explored new fields of biology — his early work in the 1960s dealt with classical molecular biology and the genetic code (the origins of which continued to fascinate him for the rest of his life). He then transfered to the study of the ribosome and its structure, which in turn led to his study of 16S and its evolutionary implications. In the 1990s, when I worked with him, he was a pioneeering microbial genomicist and collaborated with TIGR to sequence the first two Archaeal genomes. And in his final years he focused on early evolution and the last common ancestor of life in the light of what genomics has taught us.

Carl also had his humorous and counter-cultural side. I remember him telling me how his lab in the 1960s heard about the rumor that compounds in banana peels were a legal narcotic and how they launched an unofficial research project to isolate these. His verdict was that there was nothing there and neither the peels nor anything in them could get you high — but he wanted to empirically test that. Also, when reading about a supposed “Qi master” who claimed to be able to influence mutation rates with his mind, he invited him to the lab to give a demonstation — which naturally failed to show any effect under controlled conditions — but he wanted to see if the guy could really do it.

Genomics, metagenomics, and evolutionary biology has lost one of its greats — but his legacy lives on.

JCVI Viral Finishing Pipeline: a Winning Combination of Advanced Sequencing Technologies, Software Development and Automated Data Processing

JCVI viral projects are supported by the NIAID Genomic Sequencing Center for Infectious Disease (GSCID). The viral sequencing and finishing pipeline at JCVI combines next generation sequencing technologies with automated data processing. This allowed us to complete over 1,800 viral genomes in the last 12 months, and almost 8,800 genomes since 2005.

Viral Projects at JCVI

JIRA Viral Sample Tracking Workflow

Our NextGen pipeline, which utilizes SISPA-generated libraries with Roche/454 and Illumina sequencing, enables us to complete a wide variety of viral genomes including challenging samples. Automated assembly pipeline employs CLCbio command-line tools and JCVI cas2consed, a cas to ace assembly format conversion tool. Our complimentary Sanger pipeline software is currently being integrated with the NextGen pipeline. This will improve our data processing and will allow us to use validation software (autoTasker) more efficiently.

Assembly of Repetitive Viral Genomes

Genome Organization of Varicella-Zoster

Assembly of Novel Viral Genomes

CLC Assembly Viewer Representation

Promoter of Bat Genome

Promoter of Bat Genome

During the past year we have found that novel viruses, repetitive genomes, and mixed infection samples could not be easily integrated with our high-throughput assembly pipeline. We have developed an assembly and finishing process that utilizes components of the high-throughput pipeline and combines them with manual reference selection and editing. Using this approach we completed novel adenovirus genomes and mixed-infection avian influenza genomes, and improved assemblies of previously unknown arbovirus genomes. We are currently working on optimizing and automating this new pipeline.

Assembly of Mixed Viral Genomes

Consed Representation of Mixed Viral Sample

Consed Representation of Mixed Viral Sample

Repetitive genomes have long been known to present great challenges during assembly and finishing. We are presenting a new approach to assembly and finishing of repetitive varicella genome that is based on separating it into overlapping PCR amplicons followed by merging sequenced amplicons during assembly.

To streamline our viral pipelines, we have fully integrated them with JCVI’s LIMS and JIRA Workflow Management to create a semi-automated tracking interface that follows the progress of viral samples from acquisition through to NCBI submission. This allows us to process a large volume of samples with limited manual interaction and, at the same time, gives us flexibility to work on challenging and novel genomes.

Acknowledgements

The JCVI Viral Genomics Group is supported by federal funds from the National Institute of Allergy and Infectious Disease, the National Institutes of Health, and the Department of Health and Human Services under contracts no. HHSN272200900007C.

Bat coronavirus project is collaboration with Kathryn Holmes and Sam Dominguez, University of Colorado Medical Center.

The authors would like to thank members of the Viral Genomics and Informatics group at JCVI.

References

Viral genome sequencing by random priming methods. Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ. BMC Genomics. 2008 Jan 7;9:5A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species.  Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J.

Note

This post is based on a poster by Nadia Fedorova, Danny Katzel, Tim Stockwell, Peter Edworthy, Rebecca Halpin, and David E. Wentworth.

Biowalk of Fame

There is a new “Biowalk of Fame” in Maryland, and our own Craig Venter was one of the first honorees receiving a plaque, which is there for all to see as you stroll through lovely Silver Spring.

Etching of Dr. J. Craig Venter on Biowalk of Fame

Etching of Dr. J. Craig Venter on Biowalk of Fame

Other honorees include Dr. Martin Rodbell and Ben Carson. The event to honor the awardees was on April 22, which also it happens to be Earth Day. Although it rained heavily throughout the event, there were a large number of people in attendance including several local government officials including Council member Valerie Ervin and Chairman Ike Leggett. Dr Martine Rothblatt, CEO of United Therapeutics, emceed the event.

Biowalk of Fame tour sign

Biowalk of Fame tour sign

The idea behind the BioWall and the Biowalk is very innovative. The Wall is a live movie like screen that allows videos from students and the public that relate to science to be continuously aired. A student observing a paramecium under the microscope for example can mail the clip in to United Therapeutics, and it will be available for all to see. The Biowalk also has plaques dedicated to those who have made the most outstanding contributions to the State of Maryland in the sciences – hence Craig.

Dr. J. Craig Venter's plaque on the Biowalk of Fame

Dr. J. Craig Venter's plaque on the Biowalk of Fame

Biowalk of Fame

Biowalk of Fame

The take home message is, if you are wondering through Silver Spring do not be surprised if you see Craig’s name on a plaque on 1040 Spring Street. Congratulations!

Scientist Spotlight: Meet David Wentworth

During the height of the H1N1 Flu pandemic, David Wentworth was running a microbial genetics laboratory at the Wadsworth Center, New York State Department of Health (NYSDOH) where he was instrumental in developing a method to amplify influenza genomes regardless of strain using “universal primers” or short strands of DNA that recognize conserved segments across the genomes of many different flu strains. This amplification process was developed to generate recombinant influenza A viruses (the most common flu type affecting humans and animals) that could be used for the production of new vaccines. From a clinical swab it took his team 9-12 days to develop vaccine seed stocks. It was this work that first brought Dave to JCVI’s attention.

Several years ago Dave began collaborations with JCVI scientists to sequence human and avian influenza viruses. The collaborations intensified two years ago when all pandemic flu samples (or suspected flu samples) were first sent to Dave’s lab so the virus could be amplified in sufficient quantities for sequencing using his new amplification pipeline. The amplification took only a day and then isolated, non-infectious, DNA was sent to JCVI for sequencing. JCVI was the natural choice for this work since we are host to the government-funded “Influenza Genome Sequencing Project,” with the goal of sequencing large numbers of viral genomes to help scientists worldwide to understand how flu viruses evolve and cause disease. JCVI researchers then deposited influenza sequences into GenBank within two days of receiving DNA from Dave’s lab, enabling researchers worldwide to track what strains are circulating and how they are evolving. JCVI has sequenced over 75% of the influenza genomes in GenBank, the NIH public repository for sharing genetic sequencing data.

Influenza Genome Amplification Directly From Clinical Specimens

Influenza Genome Amplification Directly From Clinical Specimens (Zhou, B., M. E. Donnelly, D. T. Scholes, K. St.George, M. Hatta, Y. Kawaoka, and D. E. Wentworth. 2009. J.Virol. 83:10309-10313.).

Dave was soon invited for a talk at JCVI. “The opportunities at JCVI were to help build the [viral genomics] program. And already good, quality people are here studying viruses with a focus on viral evolution and sequencing analysis,” Dave remarked. “Being part of generating that information, I think makes you have a better feel for the biology.” The capabilities for viral sequencing combined with IFX strengths and the interest in viral evolution at JCVI was a draw for Dave and he soon joined the team. Moreover, there are opportunities at JCVI to work with collaborators who send specimens from various regions of the world for sequencing so that we can “more deeply understand the mutations that contribute to virulence,” he said. He is particularly interested in antigenic drift (how viruses escape immunity) that contributes to the “annual influenza escape,” which is critical in developing vaccine strains.

New Live Attenuated Vaccine Approaches

New Live Attenuated Vaccine Approaches. Figure shows influenza RNA polymerase activity (GFP) at various temperatures. Mutations engineered into the genome (PB1-Mut3, PB2-Mut4) synergize and inhibit replication at higher temperatures of the lung (37 C) or fever (39 C).

The need for new and improved methods to develop vaccines, coupled with the advances in synthetic genomics developed at JCVI led to the formation last year by JCVI and the company Synthetic Genomics Inc. of a new company, Synthetic Genomics Vaccines Inc. (SGVI). JCVI scientists, through SGVI, are working on a three-year collaboration agreement with Novartis to apply synthetic genomics tools and technologies to accelerate the production of the influenza seed strains required for vaccine manufacturing. The agreement, supported by an award from the U.S. Biomedical Advanced Research and Development Authority (BARDA), could ultimately lead to a more timely and effective response to seasonal and pandemic influenza outbreaks. The idea is to create viruses de novo or synthesize genes critical for its antigenicity and put these in normal vaccine strains for production. The goal of the work at SGVI is to synthesize a virus in one week, or rather a seed stock, which still needs to be amplified in big fermenters. New seed stocks take 3-4 weeks to produce which is currently a rate liming step.

You don’t hear too many people singing its praises and saying “I love the flu!” as Dave has remarked, but put in context, his enthusiasm for his work shines through best when talking about his love of teaching. He gets excited teaching young scientists about virology, especially helping them to understand the important areas to study, and where the research will lead to solve a major problem. “The rewarding part of being a mentor is to see all of the people who have found their niche – it might not be bench research but they are still carrying knowledge with them.”

David Wentworth DEW checking a hive in the late Spring.

David Wentworth DEW checking a hive in the late Spring.

Aside from spending time with his family, Dave enjoys a hobby started by his dad – to cultivate honey bees. A community gardens group at a middle school in Albany, NY was looking for bees to pollinate their plants. Dave spearheaded the effort and used it as a learning tool for kids, who helped feed honey to caterpillars and moths. He also used to give lectures on bee cultivation and has taught college courses in animal science. Dave’s enthusiasm for science among his students and peers could be considered infectious, just like the subject of his research!

Going west!

After saying good bye to our new friends in Rostock/Warnemünde I was looking forward to coming back to Swedish waters, this time a bit saltier, on the west coast. There are two marine field stations on the Swedish west coast belonging to The Sven Lovén Center for Marine Sciences. Our first stop was in station Kristineberg, beautifully situated just opposite of Lysekil, a major tourist destination in this part of Sweden. Kristineberg is yet another historical marine field station, founded in 1877. We were greeted by Professors Mike Thorndyke, head of the Kristineberg Marine Genomics group, and Katarina Abrahamsson, head of the station. The next morning we headed out together with Mike, Katarina and a couple of other local scientists to sample in Gullmarsfjorden, a 25 km fjord with a shallow threshold entrance and a maximum depth of almost 120 meters, resulting in a highly stratified water column.

When we got back from sampling we had a chance to get a tour of the station and after the crew were invited for a lovely dinner and got to try some delicious Swedish west coat shrimp.

Mike Thordyke and Katarina Abrahamsson giving a tour of Kristineberg research station to the Sorcerer II crew.

Mike Thordyke and Katarina Abrahamsson giving a tour of Kristineberg research station to the Sorcerer II crew.

When the time came to get going the staff in Kristineberg suggested that we make another stop on our way to Oslo, in Tjärnö the other marine research station on the west coast. I was excited to go back to Tjärnö because about 10 years ago I spent a couple of weeks there when taking an undergraduate ecology course.

Head of the station, Professor Kerstin Johannesson welcomed us when we arrived and within an hour a large crowd of curious staff and students had gathered around the boat and were invited onboard for a tour. Kerstin reciprocated by showing us around the station. The crew particularly enjoyed the petting zoo aquarium where we could play with sea stars and sea cucumbers!

It was a beautiful quite night and I went kayaking around the small islands nearby.

Karolina in the kayak. Photo by John Henke, Sorcerer II first mate.

Karolina in the kayak. Photo by John Henke, Sorcerer II first mate.

The next day we picked up a sample outside the station and continued north through the Oslo fjord, the weather was spectacular and logistics coordinator Sarah Dyste and I decided to jump in the refreshing water for a swim.

Sorcerer II is now docked in Oslo, right in front of Town hall, were we just had and amazing tour and were invited to meet the deputy mayor of Olso. He was curious about our research and also told us a lot about Oslo’s interesting history.

The time has come for me to say good bye to the rest of the crew and fly home to Stockholm, where I will continue my cyanobacteria projects in the lab. It has been an absolutely amazing summer and I can’t wait to get back to the boat in later this year to meet with Mediterranean collaborators and get ready for sampling in the Med in 2010!

Bye for now,

Karolina