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Thursday, August 21, 2014

Biomathematics: the great frontier of the 21st century?

Some argue that by 2100 biology and mathematics will have changed each other dramatically.

Once upon a time, biology meant zoology and botany, the study of animals and plants. The invention of the microscope shifted the emphasis to the level of cells, and more recently the focus has been at the molecular level. Traditionally, the life sciences were attractive for young people who were passionate about science but who disliked mathematics or felt they were not good at it. But mathematics now plays a vital role in biology, and students need mathematical skills.

Biological systems are hugely complex, but simple mathematical models can isolate and elucidate key elements and processes and predict crucial aspects of behaviour. Many problems in biology have been solved using mathematics already developed in other areas – network analysis, group theory, differential equations, probability, chaos theory and combinatorics – but completely new mathematical techniques may be required to solve some tough problems in the life sciences.

The shape of a protein is an essential factor in determining its functions. For example, haemoglobin has a complex folded shape that enables it to "pick up" an oxygen molecule and "drop it" where it is needed. The folding and tangling of protein molecules is being modelled using the branch of topology called knot theory.

Network analysis shows us that a large network of simple components – whether transistors or neurons – can exhibit astonishingly complex behaviour. The human brain has 100 billion nerve cells, linked together by a biological wiring system of axons and dendrites. The number of interconnections is vast, something like a thousand million million. This is "big data" with a vengeance.

One simple element can do little. Link a large number together and you can get fantastically complex behaviour. For the brain, this includes thinking. Many questions in neuroscience remain to be answered, such as "how does memory work?" How is information from the senses interpreted and stored? Bio-informatics deals with the enormous data sets produced in biological research.

Systems biology is a rapidly developing interdisciplinary field of biological research. It focuses on complex interactions using a holistic approach aimed at discovering and understanding emergent properties of organisms. Such properties are difficult or impossible to understand using a reductionistic approach – breaking them down into basic constituents. Systems biology makes extensive use of mathematical and computational models.

The communication networks in the human body involve millions of interlinked cells. Occasionally, these networks break down, causing diseases such as cancer. Systems Biology Ireland, at UCD, is designing new therapeutic approaches based on a systems-level, mechanistic understanding of cellular networks. Researchers at Systems Biology apply mathematics and computer science to enormous data sets arising from biological techniques. Their research aims to find out what genes do, how they work together, what goes wrong in diseases, and how to cure them.

Just as astronomy gave rise to spectacular developments in mathematical analysis in the 18th century, biology may have a profound effect on mathematics in the future. Some commentators see biomathematics as the great frontier of the 21st century, and argue that by 2100 biology and mathematics will have changed each other dramatically, just as mathematics and physics did in earlier centuries.

Peter Lynch is professor of meteorology at University College Dublin. He blogs at thatsmaths.com
URL: http://www.irishtimes.com/news/science/biomathematics-the-great-frontier-of-the-21st-century-1.1898160

Contact Person: Peter Lynch (peter.lynch@ucd.ie)

Why biosciences and engineering are on a collision course

USC goes all in on convergent bioscience, bringing scientific curiosity and engineers' know-how to solve medical problems.

The world has become an enormously complex place. In 1790, the U.S. Patent Office opened its doors, and it took 103 years for the office to issue its first half-million patents. Now it issues far more than that in a single year.

And this acceleration toward complexity isn't just about patents — it's also about the science that drives them. That's especially pronounced in biomedicine. A century ago, a physician was everything in a town. He (or she) would deliver babies, dispense medication to the ill and even tend to a dog's broken leg. Today, doctors are so specialized they can be experts on a disease like cancer, for example, in only certain parts of the body, such as the bones, in a specific segment of the population, like children. They may do research too.

That specialized knowledge has led to big advances, but there's a flip side: These highly specialized scientists risk becoming so isolated that they might miss suggestions from others that could turn dead ends into new, promising research directions. It turns out that as our explorations peel away an ever-more intricate world, the connections between experts with wide-ranging perspectives become more vital. At USC, a movement is underway to bring together bioscientists and engineers to make the next generation of great leaps. It's called convergence, and it melds three fields: life science, physical sciences and engineering.

Society needs convergent research to move innovation forward and fix difficult challenges, but greater coordination is needed, according to a 2014 report from the National Research Council. It's going to take a culture shift for universities.

To understand how we got here, it helps to look to the past. The world of biology used to be rather flat, says Susan Forsburg, professor of biological sciences at the USC Dornsife College of Letters, Arts and Sciences. Biologists mostly studied how living organisms looked and behaved, and didn't have a clear way to "get under the hood" to examine the molecular mechanisms that explained those behaviors. But during World War II, physicists got involved and shook up the field. They became interested in the mechanics of DNA.

In 1953, physicist Francis Crick teamed up with James Watson to crack the structure of DNA. Driven by new ideas, scientists then figured out how DNA works, changing biology forever and giving rise to an entirely new field: molecular biology.

"Biology quickly went from observational science to something that used quantitative molecular approaches," Forsburg explains. The understanding of disease shifted dramatically as well. To cure someone of a disease, it became necessary to take that illness apart, cell by cell and gene by gene.

More recently, a genomics revolution has swept the sciences since the first map of the human genome was published in 2001. Sequencing an organism's entire genome and pinpointing sequence differences has offered insights into the foundation of many diseases and suggested potential solutions.

"The Human Genome Project gave us a parts list for understanding living systems, and what we want to do now is understand what the instruction manual looks like," says Steve Kay, dean of USC Dornsife.

Engineers have started bringing their own knowledge and skills to biological research as well. Take nanotechnology, which spurred new tools and understanding of the world on a tiny scale. Researchers have already created teeny particles that deliver drugs to targets inside the body. They're even exploring using nanosponges to stop internal bleeding.

The stage is now set for the next wave of change, melding engineers, molecular biologists and geneticists. Researchers call this wave convergence, and it relies on specialists working side by side. "The way you approach a problem is a team atmosphere, and the tools are new, so it can't be effective through virtual connections between people," Kay says. "Convergence needs a venue to be effective—a venue for really smart scientists and engineers to approach problems that are relevant to medicine."

USC in 2103 recruited biologist and interdisciplinary bridge-builder Scott Fraser from Caltech to help bring these experts together as director of science initiatives within the USC Office of the Provost. He's uniting physicists and engineers, computational biologists and chemists, and that's just for starters. Already, he and fellow faculty have begun bringing in the latest scientific equipment — including one of the world's most powerful experimental microscopes — that they'll all share, whether they come from biology, engineering or another field.

The new faculty, new equipment and new cooperation are evidence that the age of scientific silos is over. Forsburg, for one, relishes it, and she's quick to cite another example of convergence from her discipline of biological sciences.

"If you look at the acronym MCB at USC, here that stands for 'molecular and computational biology,'" she says. "Our math-oriented colleagues help us make sense of those big data sets. We're always looking for anything that mixes the pot and makes great synergy possible."

It hasn't always been easy to cross-pollinate different arenas of science. Mark Thompson, a chemist and materials scientist at USC Dornsife and USC Viterbi School of Engineering, says that when he started his career in 1987, scientists strived to be the sole authors on research papers. Forget collaborating with peers in your department, much less with researchers in other fields across campus. "Fortunately, we've moved away from that model," he says.

With researchers today more open to working together, big ideas from one scientific field can quickly translate into others, says Michael Quick, executive vice provost and professor of biological sciences. "I think we're about to see an increase in the number of practical solutions to problems coming at a faster rate," he says.

Part of the challenge is time and communication, Quick says. Physicians might have ideas that could help scientists, but they're busy with patients. And scientists and engineers aren't aware of the essential problems physicians need to solve.

But Yannis C. Yortsos, dean of USC Viterbi, says that the explosive pace of science and engineering has radically transformed all fields, including medicine. More than ever before, experts are working together to condense the time between scientific discovery, technology development and its application. "In the past, it took a long time for something to become useful," Yortsos says. "Today, the distance between the discovery of a phenomenon and its leveraging for useful purposes has shrunk dramatically. This is particularly important for interdisciplinary work, where people work and innovate closely together."

Take the artificial retina, for example. The implanted device helps restore vision. Led by University Professor Mark Humayun, a team of engineers, ophthalmologists, computer scientists and biologists from USC, other universities and industry have come together to invent, test and perfect the device.

The researchers had to bridge cellular biology — necessary for understanding how to stimulate retinal cells without permanent damage — with microelectronics, which led to the miniaturized, low-power integrated chip that converts signals and stimulates the cells. The hardware had to work seamlessly with software processing and tuning algorithms, and the whole package had to operate inside the eye. Then the team had to figure out how to surgically integrate the device inside the body, making sure that its 1,000 electrodes were placed in the exact spot in the eye only 6 millimeters across.

The U.S. Food and Drug Administration approved the device in 2013, and physicians are now implanting it into patients.

Finding clean and sustainable energy. Fighting disease. Feeding a growing world population. Which of these problems might convergence begin to solve? Perhaps all of them, and more.

Thompson already lives out the movement every day. With his USC Dornsife and USC Viterbi colleagues, he's used chemistry and engineering to create a way to light up smartphone screens four times more efficiently than ever — a technology now used by Samsung. He's also working on lightweight, portable solar energy cells. Yet he's just as excited about the potential for convergence to boost human health.

"We're almost at the point where we can sequence someone's genes and identify the best drug based on the person's genetic makeup," Thompson says. "So, as we understand the human body better, it's going to lead to revolutionary things."

Convergence will usher in a new generation of investigators who are uniquely prepared to work together and tackle challenges. "The students, both graduate and undergrads, they're not going to think of themselves as a chemist or a biologist," Kay says. "They're going to think of themselves as a problem-solver."

This story originally appeared in the summer 2014 issue of USC Trojan Family Magazine.
URL: http://www.news.usc.edu/67061/why-biosciences-and-engineering-are-on-a-collision-course/

Contact Person: Katharine Gammon (kategammon@gmail.com)

Tuesday, August 19, 2014

Call for Nominations--2015 Alan T. Waterman Award

2015 Alan T. Waterman Award

~ The National Science Foundation's Highest Honor ~

Call for Nominations http://www.nsf.gov/od/waterman/nsf_watermanaward_2015callfornominations_140806.pdf

Deadline: October 24, 2014

The National Science Foundation is pleased to accept nominations for the 2015 Alan T. Waterman Award. Each year, the Foundation bestows the Waterman Award to recognize the talent, creativity, and influence of a singular young researcher. The award consists of a $1,000,000 prize, a medal, a certificate, and a trip for two to Washington, DC, to receive the award. For details about the Waterman Award's history, the nomination procedure and the selection criteria please visit http://www.nsf.gov/od/waterman/waterman.jsp.

Nominees are accepted from any field of science or engineering. Nominations must be submitted electronically using NSF's FastLane system at https://www.fastlane.nsf.gov/honawards/index.jsp.

Please direct all inquiries about the award and the nomination procedures to Mayra Montrose (mmontros@nsf.gov).
URL: http://www.nsf.gov/od/waterman/waterman.jsp.

Friday, August 15, 2014

Global Collaboration Creates First Publicly Available Illumina HiSeq X Ten DNA Sequence Dataset

Australia's Garvan Institute, DNAnexus, and AllSeq sponsor sharing of sample dataset to educate the scientific community about the potential for world's most powerful DNA sequencing platform

August 07, 2014 01:21 PM Eastern Daylight Time
SYDNEY & MOUNTAIN VIEW, Calif. & LA JOLLA, Calif.--(BUSINESS WIRE )--The Garvan Institute of Medical Research, DNAnexus, and AllSeq, today announced that they are sponsoring free access to the world's first publicly available datasets generated using the Illumina HiSeq X Ten DNA sequencing platform. The goal for this project is to provide researchers with sample data that will allow them to gain a deeper understanding of what this technological advancement might mean for their work today and in the future.

"The tremendous advances in both volume and cost of whole genome sequencing using the Illumina HiSeq X Ten platform provides an exciting and practical avenue that moves us closer to the clinical translation of genomics"

The Garvan Institute's Kinghorn Centre for Clinical Genomics in Sydney, Australia, was one of the first three organizations in the world to acquire the Illumina HiSeq X Ten sequencing system. In an effort to enable the scientific community to assess data quality from an independent laboratory, they have made reference datasets available for a world first HiSeq X Ten data sharing project.

DNAnexus, an enterprise solution for genome informatics and data management, has sponsored the data storage and downloading support. The company also ran analyses to produce quality metrics to help the scientific community understand the results. AllSeq, which created the Sequencing Marketplace for matching DNA researchers and their needs with next generation sequencing service providers, arranged this data sharing endeavor as a part of its effort to educate scientists about different sequencing technologies and what they are suitable for.

"The tremendous advances in both volume and cost of whole genome sequencing using the Illumina HiSeq X Ten platform provides an exciting and practical avenue that moves us closer to the clinical translation of genomics," said Associate Professor Marcel Dinger, Head of Clinical Genomics and Genome Informatics at the Garvan Institute. "Advancing genomic medicine remains an international and highly collaborative effort and the Kinghorn Centre for Clinical Genomics is pleased to be working with DNAnexus and AllSeq to make sample data available to clinicians and researchers so that they can gain a deeper understanding of how this powerful technology may impact their work."

To develop the sample datasets, Garvan scientists used the Coriell Cell Repository NA12878 reference sample, which has been extensively analyzed by the Genome in a Bottle Consortium. Two different, high quality datasets are provided (NA12878D and NA12878J), each of which was sequenced on a single lane of an Illumina HiSeq X patterned flow cell, achieving over 120 Gb of yield, with greater than 87 percent bases with quality greater than Q30 in just 2.8 days. Each dataset meets the minimum coverage and quality guaranteed by Illumina and is indicative of the potential for the Illumina HiSeq X Ten sequencing system.

As the study and application of genomic data expands and proliferates, its true promise hinges on the genomics community's collective ability to manage all these data —securely, collaboratively, and efficiently. At full capacity, the Illumina HiSeq X Ten platform generates one genome every 25 minutes. According to internal data, transferring the two test genomes used in this project from the Garvan Institute in Australia into the DNAnexus system took less than 50 minutes, demonstrating that the DNAnexus platform in conjunction with Amazon's AWS Cloud can keep up with the pace of genomics. The runs were then analyzed and instantly shared with Garvan's scientific team for review. Within hours, these data were made available to the global research community to view and download.

"The DNAnexus platform was designed to be a complete solution for genomics analysis and data management, helping to accelerate basic science and clinical breakthroughs by bringing diverse teams together around ever-growing genomic datasets. The HiSeq X Ten presents a further challenge and opportunity for genomics in the production and management of genomic data, and Garvan has shown that the cloud can rise to this challenge," said Richard Daly, CEO of DNAnexus. "With the rise of consortia in the genomics community, the inevitability of the cloud and its ability to leverage scientific collaboration is near term. We are pleased to be working with the Garvan Institute and AllSeq to host the world's first HiSeq X Ten data sharing project so the scientific community can take a closer look at results from the '$1000 genome'."

The original FASTQ files, as well as analysis results (BAM and VCF files) and quality metrics, were calculated using the tools FastQC and Picard, (e.g., MarkDuplicates, CollectInsertSizeMetrics, and CollectWgsMetrics), are available at http://allseq.com/x-ten-test-data .

Those with DNAnexus accounts can also access these data via the DNAnexus platform, where users are able to copy any of the files to their own DNAnexus projects for further downstream analysis. For more information, https://dnanexus.com .

About the Garvan Institute of Medical Research and its Kinghorn Centre for Clinical Genomics

The Garvan Institute of Medical Research is one of Australia's largest medical research institutions with more than 600 scientists, students and support staff. Garvan's main research areas are: Cancer, Diabetes & Metabolism, Immunology and Inflammation, Osteoporosis and Bone Biology, and Neuroscience. Garvan's mission is to make significant contributions to medical science that will change the directions of science and medicine and have major impacts on human health. The outcome of Garvan's discoveries is the development of better methods of diagnosis, treatment, and ultimately, prevention of disease. In 2012, Garvan established Australia's first purpose-built facility for undertaking clinical-grade genome sequencing and large-scale research projects. With the support from the Kinghorn Foundation, Garvan acquired an Illumina HiSeq X Ten Sequencing System in January, 2014. The Kinghorn Centre for Clinical Genomics (KCCG) researchers undertake collaborat ive projects and genome-based studies to improve genome interpretation, with the ultimate aim of advancing the use of genomic information in patient care. KCCG is seeking accreditation that would ultimately allow clinicians to sequence genomes for diagnostic and therapeutic purposes. For more information please visit: http://www.garvan.org.au/

About DNAnexus

DNAnexus is powering the genomics revolution with an enterprise-level solution that combines cloud computing with advanced bioinformatics. The DNAnexus team is made up of experts in software, computational biology, and genetics who are on a mission to establish DNAnexus at the center of a growing ecosystem of scientific and clinical research, and diagnostic efforts in personalized medicine. For more information please visit: https://dnanexus.com .

About AllSeq

AllSeq has created the world's first true Sequencing Marketplace, which helps researchers fulfill their sequencing needs by matching them with the appropriate pool of sequencing providers. They provide free online tools for describing sequencing projects in an easy and systematic way, ensuring estimates are easy to compare and allowing researchers to pick the best provider (based on price, technology, turnaround time, etc). AllSeq also maintains the NGS Knowledge Bank, a neutral source of information on sequencing technologies, platforms and applications. For more information, please visit http://allseq.com .
URL: http://allseq.com/x-ten-test-data

Contact Person: Shawn C Baker (info@allseq.com)

Wednesday, August 6, 2014

The Federation of American Societies for Experimental Biology (FASEB)'s third annual BioArt competition

The Federation of American Societies for Experimental Biology (FASEB) is pleased to announce its third annual BioArt competition. Each day, scientific investigators product thousands of images and videos as part of their research, but very few are ever seen outside the laboratory. We are looking for visually compelling, high resolution submissions from federally-funded researchers and/or FASEB constituent society members. Images and videos can be submitted through August 30, 2014. For more information or to enter, please visit: www.faseb.org/bioart.

Please help us spread the word about this competition! Contact us at bioart@faseb.org if you would like a pdf flyer to share with others.
URL: http://www.faseb.org/About-FASEB/Scientific-Contests/BioArt.aspx

Contact Person: Joseph R. Haywood, PhD (bioart@faseb.org)