The concept of using lasers to synthesize DNA with a specified genetic sequence intrigued me so much that I tried to describe it in my October Photonic Frontiers feature . After receiving a grant from the National Science Foundation , the company behind the idea, Cambrian Genomics (San Francisco, CA), has released new details on the process, and my speculation about its nature turned out to be wrong.
Previously, DNA synthesis has been a two-stage assembly process. First individual base pairs are assembled into "oligonucleotide" sequences of 60 to 100 base pairs. Then, a number of those longer chains are stitched together into the synthetic DNA. The process is time-consuming and costs 30 to 50 cents per base pair, a number which adds up for long sequences. I had thought they might be using lasers to manipulate the base pairs into place.
Instead, Cambrian Genomics uses microarray cloning to mass-produce a million oligonucleotides in parallel, a process that has been tried before, but was hampered by the high error rates of microarray synthesis. To overcome that problem, Cambrian synthesizes large volumes of oligonucleotide fragments on microarrays, then uses massively parallel DNA sequencing to sort the different DNA variants and identify those with the desired sequence. Then, says Cambrian founder and CEO Austen Heinz, "we use laser catapulting, also known as laser-induced forward transfer, to eject clonal DNA populations," which were identified as having the desired sequences. The process is a variation on laser capture microdissection , which can excise part of a cell and move it to a desired location without damaging DNA. High-speed laser pulses then eject beads carrying the desired sequences in the right order to assemble into genes on a 384-well plates.
Cambrian Genomics process uses lasers to select oligonucleotides with the desired sequence. The goal, Cambrian wrote in a summary of its application for a phase-one Small Business Innovation Research (SBIR) grant, "is to be able to recover tens of thousands of sequence-verified oligonucleotides in several hours from sequencer flowcells." NSF announced on December 5, 2012, a $150,000 grant that will run through the first six months of 2013. Cambrian hopes that will open the door to disruptive reductions in the cost of DNA synthesis.
Thousands of planets are now known outside our solar system, from rocky worlds to "hot Jupiters" to planets orbiting not one, but two stars. So where did all this diversity come from? Join us for a conversation about how planets form, complete with data from the Hubble and Spitzer Space Telescopes, as well as ground-based scopes. See new images and 3-D computer models astronomers are using to try to learn how planets are born into such diversity.
This course of 25 lectures, filmed at Cornell University in Spring 2014, is intended for newcomers to nonlinear dynamics and chaos. It closely follows Prof. Strogatz's book, "Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering."
The mathematical treatment is friendly and informal, but still careful. Analytical methods, concrete examples, and geometric intuition are stressed. The theory is developed systematically, starting with first-order differential equations and their bifurcations, followed by phase plane analysis, limit cycles and their bifurcations, and culminating with the Lorenz equations, chaos, iterated maps, period doubling, renormalization, fractals, and strange attractors.
A unique feature of the course is its emphasis on applications. These include airplane wing vibrations, biological rhythms, insect outbreaks, chemical oscillators, chaotic waterwheels, and even a technique for using chaos to send secret messages. In each case, the scientific background is explained at an elementary level and closely integrated with the mathematical theory. The theoretical work is enlivened by frequent use of computer graphics, simulations, and videotaped demonstrations of nonlinear phenomena.
The essential prerequisite is single-variable calculus, including curve sketching, Taylor series, and separable differential equations. In a few places, multivariable calculus (partial derivatives, Jacobian matrix, divergence theorem) and linear algebra (eigenvalues and eigenvectors) are used. Fourier analysis is not assumed, and is developed where needed. Introductory physics is used throughout. Other scientific prerequisites would depend on the applications considered, but in all cases, a first course should be adequate preparation.
What is time-reversal symmetry? How to find whether electron is perfectly round or not? Professor of Physics at Harvard University John Doyle discusses the Big Bang, time-reversal symmetry, and the electric dipole moment of the electron.
We see antimatter in experiments on Earth, but we have to create that antimatter using a very high-energy experiments. So we know that antimatter exists, we know that antimatter has almost exactly the same properties as matter. That means we can, for every particle of matter that we know about, like the proton or the electron, there is a corresponding antiparticle, antiproton, anti-electron. This is well-known. And the particles and antiparticles, say, the proton and the antiproton, have the same mass, they have the same charge, they have the same magnetic moment.
Time-reversal symmetry is very easy to see mathematically, a little bit harder to see physically. So mathematically one has a set of equations, physics equations, like force equals mass times acceleration, or conservation of energy. And we can use these equations to predict, for example, the path a ball takes as it bounces along the ground, or some other physical phenomenon. Now, if we look at those equations and we replace time by minus time, what we find is that the equations behave almost exactly the same. In other words, in the most common cases, in some parts of classical physics they behave exactly the same.
If the electron not only has a magnetic moment but also has an electric dipole moment, that means that the electron is not perfectly round, but it’s a little bit oval, then that’s an equivalent to having an extra positive charge here and a little bit of extra negative charge there. And that’s what we call an electric dipole. Now you can imagine, if the electron has an electric dipole and we reverse time, nothing happens. With the magnetic dipole the curving goes in the opposite direction, but if I reverse time, then the charge simply stays still. And because the electric dipole would not change, but the magnetic dipole would change, that violates time-reversal symmetry.
Matthew Cobb is Professor of Zoology and a senior lecturer in animal behaviour at the University of Manchester. After spending some time researching humans at the institute of psychiatry, a lot of his work now investigates insect behaviour and its evolutionary and genetic basis, particularly smell.
Dr. Doudna, who specializes in the study of RNA, will present a brief history of the bacterial RNA-guided CRISPR biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism. Using CRISPR-Cas "clustered regularly interspaced short palindromic repeats" technology provides the foundation for remarkable developments in modifying, regulating, or marking genomic loci in a wide variety of cells and organisms. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way to fundamental discoveries in biology with applications in all branches of biotechnology, and strategies for human therapeutics. Dr. Doudna will discuss recent findings regarding the molecular mechanism of Cas9 and its use for targeted cell-based therapies.
About the annual Margaret Pittman Lecture: This annual lecture honors Dr. Margaret Pittman, NIH’s first female lab chief, who made significant contributions to microbiology and vaccine development, particularly in the areas of pertussis and tetanus, during her long career at the National Institute of Allergy and Infectious Diseases.
Author: Jennifer Doudna, Ph.D., Li Ka Shing Chancellor's Chair in Biomedical Sciences and Professor, Department of Molecular and Cell Biology and Department of Chemistry at the University of California, Berkeley; Investigator, Howard Hughes Medical Institute
The news media in recent months have been full of dire warnings about the risk that AI poses to the human race, coming from well-known figures such as Stephen Hawking, Elon Musk, and Bill Gates. Should we be concerned? If so, what can we do about it? While some in the mainstream AI community dismiss these concerns, I will argue instead that a fundamental reorientation of the field is required.
Stuart Russell is one of the leading figures in modern artificial intelligence. He is a professor of computer science and founder of the Center for Intelligent Systems at the University of California, Berkeley. He is author of the textbook ‘Artificial Intelligence: A Modern Approach’, widely regarded as one of the standard textbooks in the field. Russell is on the Scientific Advisory Board for the Future of Life Institute and the Advisory Board of the Centre for the Study of Existential Risk
Since the publication of the human genome in 2001, there has been a fundamental shift in molecular biology research from small scale, hypothesis focused science to larger scale hypothesis generating science. I will describe some of the key components of the last decade's research in this area, including Genomewide Association, the 1,000 genomes project and the ENCODE project and the way these projects draw on cutting edge statistics and algorithm processes. I will then describe the current excitement in applying this to medical issues, with speculation about how the next decade will develop in genome medicine.
About the Speaker
Dr. Birney is Associate Director of the EMBL-EBI. Before taking up his current post, he developed a number of databases (such as Ensembl), and worked on specific genomics projects, ranging from the Human Genome sequencing in 2000 through to the ENCODE project. For ENCODE he coordinated the analysis for both the 1% Pilot (published in 2007) and the scale up (likely to be published in 2012).
As Associate Director, Dr Birney takes a strategic oversight role of the EBI services alongside Rolf Apweiler (the other Associate Director of the EBI). This ranges from genome sequences through proteins, small molecules, macromolecular structures to networks, pathways and systems.
Dr Birney still runs a research group which focuses on genomic algorithms and studying inter individual differences, in both human and other species.
Light speed is one of science fiction’s major plot limitations — and maybe one of the major limitations of science. How can we explore the stars if it takes tens of thousands of years to get to them… or the galaxies, if it takes billions of years? Warp drives and wormholes are often co-opted by authors to save the day — but what is scientific, and what is make-believe? General relativity allows space and time to bend. Can we say there are limits, or is the answer as yet unknown? Does faster-than-light travel mean time-travel is inevitable?
Join Tamara to explore warp drives, light-speed limits, event horizons, and perhaps even the ultimate fate of the universe.
Gravity is the most important force in the universe, holding together planetary systems, stars, and galaxies. It is what makes the stars hot enough to shine and what keeps the Earth close enough to the Sun for life to form. It is also what ends the life of every massive star with a spectacular collapse and the formation of a black hole. Finding and studying hundreds of black holes within the Milky Way and in other galaxies brings us closer to understanding gravity at its extreme.
Cosmic Origins is the story of the universe but it's also our story. Hear about origin of space and time, mass and energy, the atoms in our bodies, the compact objects where matter can end up, and the planets and moons where life may flourish. Modern cosmology includes insights and triumphs, but mysteries remain. Join the six speakers who will explore cosmology's historical and cultural backdrop to explain the discoveries that speak of our cosmic origins.
Dr. Feryal Özel, Associate Professor, Astronomy/Steward Observatory, University of Arizona.
The last century produced advances in science that would be unimaginable to earlier generations, and no achievement had more impact than the extension of human life. Innovations in medicine and sanitation saw a radical increase in lifespan leading to unprecedented global economic growth and individual opportunity. But researchers are not resting on their laurels and the search for new scientific pathways is accelerating. Advances in genomics, proteomics, informatics, computing and cell therapy technologies bring with them the likelihood of extending lifespan further -- very possibly, much further. Dr. Craig Venter and Dr. Peter Diamandis, pioneers in this emerging field, join us to explain the opportunities and challenges ahead in the search for longer and healthier lives.
Extra dimensions of space—the idea that we are immersed in hyperspace—may be key to explaining the fundamental nature of the universe. Relativity introduced time as the fourth dimension, and Einstein’s subsequent work envisioned more dimensions still--but ultimately hit a dead end. Modern research has advanced the subject in ways he couldn’t have imagined. John Hockenberry joins Brian Greene, Lawrence Krauss, and other leading thinkers on a visual tour through wondrous spatial realms that may lie beyond the ones we experience.
As the UK’s Chief Medical Officer, Dame Sally is the country’s leading figure in public health. In this lecture, she will talk about microbial resistance and the dire threat it poses if action is not taken to reinvigorate research into a new class of antibiotic.
She has described the threat posed by antibiotic resistance as being on a par with that of terrorism and climate change and warned that “Antimicrobial resistance poses a catastrophic threat. If we don’t act now, any one of us could go into hospital in 20 years for minor surgery and die because of an ordinary infection that can’t be treated by antibiotics."
Her highlighting of the issue in the CMO’s Annual Report, published in March 2013, included 17 recommendations on antibiotic resistancy, many of which are designed to tackle the ‘discovery void’ in pharmaceutical research. A year on from the report, Dame Sally will talk about the Government’s strategy for action, the challenges she faces and the progress made.
Could simple worms help unravel complex human brains? Dr. Aimee Kao, Dr. Dena Dubal and Jennifer Yokoyama explore the role genes play in the brain. Series: "UCSF Osher Center for Integrative Medicine presents Mini Medical School for the Public" [6/2013] [Health and Medicine] [Show ID: 24712].
Quantum theory has allowed scientists to understand better the subatomic world, and led to revolutionary technologies including computers, lasers and atomic clocks. In spite of its successes, quantum physics can seem strange and counterintuitive. It describes a world in which the concepts of waves and particles are deeply intertwined; and has led to the bizarre notions of superposition, which allows particles to exist in many concurrent states until observed, and entanglement, whereby particles control the state of distant and seemingly unconnected partners within a system.
Recent technological advances have allowed us to control and observe isolated quantum systems such as atoms, molecules, photons or superconducting microchips. Beyond fuelling a fundamental interest in their quantum behaviour, these advances open fascinating perspectives for new applications in which quantum strangeness could be directly harnessed to achieve tasks that are impossible with classical physics.
The age of bioengineering is upon us, with scientists' understanding of how to engineer cells, tissues and organs improving at a rapid pace. Here, how this could affect the future of our physical bodies.
Superintelligence asks the questions: What happens when machines surpass humans in general intelligence? Will artificial agents save or destroy us? Nick Bostrom lays the foundation for understanding the future of humanity and intelligent life.
The human brain has some capabilities that the brains of other animals lack. It is to these distinctive capabilities that our species owes its dominant position. If machine brains surpassed human brains in general intelligence, then this new superintelligence could become extremely powerful - possibly beyond our control. As the fate of the gorillas now depends more on humans than on the species itself, so would the fate of humankind depend on the actions of the machine superintelligence.
But we have one advantage: we get to make the first move. Will it be possible to construct a seed Artificial Intelligence, to engineer initial conditions so as to make an intelligence explosion survivable? How could one achieve a controlled detonation?
This profoundly ambitious and original book breaks down a vast track of difficult intellectual terrain. After an utterly engrossing journey that takes us to the frontiers of thinking about the human condition and the future of intelligent life, we find in Nick Bostrom's work nothing less than a reconceptualization of the essential task of our time.
The New Horizons mission will help us understand worlds at the edge of our solar system by making the first reconnaissance of the dwarf planet Pluto and by venturing deeper into the distant, mysterious Kuiper Belt – a relic of solar system formation.
Michael Mosley embarks on an informative and ambitious journey exploring how the evolution of scientific understanding is intimately interwoven with society's historical path.
Michael begins with the story of one of the great upheavals in human history - how we came to understand that our planet was not at the centre of everything in the cosmos, but just one of billions of bodies in a vast and expanding universe.
He reveals the critical role of medieval astrologers in changing our view of the heavens, and the surprising connections to the upheavals of the Renaissance, the growth of coffee shops and Californian oil and railway barons.
In human embryos, the SRY gene encodes a unique transcription factor that activates a testis-forming pathway at about week seven of development. Before this time, the embryonic gonad is "indifferent," meaning that it is capable of developing into either a testis or an ovary (Figure 2). Likewise, the early embryo has two systems of ducts, Wolffian and Müllerian ducts, which are capable of developing into the male and female reproductive tracts, respectively. Once the SRY gene product stimulates the indifferent gonad to develop into a testis, the testis begins producing two hormones, testosterone and anti-Müllerian hormone, or AMH. Testosterone and one of its derivatives, dihydrotestosterone, induce formation of other organs in the male reproductive system, while AMH causes the degeneration of the Müllerian duct. In females, who do not contain the SRY protein, the ovary-forming pathway is activated by a different set of proteins. The fully developed ovary then produces estrogen, which triggers development of the uterus, oviducts, and cervix from the Müllerian duct.
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