Lifeboat Foundation

New research by UCSF scientists could accelerate – by 10 to 100-fold – the pace of many efforts to profile gene activity, ranging from basic research into how to build new tissues from stem cells to clinical efforts to detect cancer or auto-immune diseases by profiling single cells in a tiny drop of blood.

The study, published online April 27, 2016, in the journal Cell Systems, rigorously demonstrates how to extract high-quality information about the patterns of gene expression in individual cells without using expensive and time-consuming deep-sequencing technology. The paper’s senior authors are Hana El-Samad, PhD, an associate professor of biochemistry and biophysics at UCSF, and Matt Thomson, PhD, a faculty fellow in UCSF’s Center for Systems and Synthetic Biology.

“We believe the implications are huge because of the fundamental tradeoff between depth of sequencing and throughput, or cost,” said El-Samad. “For example, suddenly, one can think of profiling a whole tumor at the single cell level.”

Many think author, inventor and data scientist Ray Kurzweil is a prophet for our digital age. A few say he’s completely nuts. Kurzweil, who heads a team of more than 40 as a director of engineering at Google, believes advances in technology and medicine are pushing us toward what he calls the Singularity, a period of profound cultural and evolutionary change in which computers will outthink the brain and allow people—you, me, the guy with the man-bun ahead of you at Starbucks—to live forever. He dates this development at 2045.

Raymond Kurzweil was born February 12, 1948, and he still carries the plain, nasal inflection of his native Queens, New York. His Jewish parents escaped Hitler’s Austria, but Kurzweil grew up attending a Unitarian church. He worshipped knowledge above all, and computers in particular. His grandmother was one of the first women in Europe to earn a Ph.D. in chemistry. His uncle, who worked at Bell Labs, taught Ray computer science in the 1950s, and by the age of 15, Kurzweil was designing programs to help do homework. Two years later, he wrote code to analyze and create music in the style of various famous composers. The program won him the prestigious Westinghouse Science Talent Search, a prize that got the 17-year-old an invitation to the White House. That year, on the game show I’ve Got a Secret, Kurzweil pressed some buttons on a data processor the size of a small car. It coughed out original sheet music that could have been written by Brahms.

After earning degrees in computer science and creative writing at MIT, he began to sell his inventions, including the first optical character recognition system that could read text in any normal font. Kurzweil knew a “reading machine” could help the blind, but to make it work, he first had to invent a text-to-speech synthesizer, as well as a flatbed scanner; both are still in wide use. In the 1980s Kurzweil created the first electronic music keyboard to replicate the sound of a grand piano and many other instruments. If you’ve ever been to a rock concert, you’ve likely seen the name Kurzweil on the back of a synthesizer.

Nice read that ties Quantum properties such as tunneling to everything around us including our own blood supply in our bodies.

Objects of the quantum world are of a concealed and cold-blooded nature: they usually behave in a quantum manner only when they are significantly cooled and isolated from the environment. Experiments carried out by chemists and physicists from Warsaw have destroyed this simple picture. It turns out that not only does one of the most interesting quantum effects occur at room temperature and higher, but it plays a dominant role in the course of chemical reactions in solutions!

We generally derive our experimental knowledge of quantum phenomena from experiments carried out using sophisticated equipment under exotic conditions: at extremely low temperatures and in a vacuum, isolating quantum objects from the disturbing influence of the environment. Scientists from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw, led by Prof. Jacek Waluk and Prof. Czeslaw Radzewicz’s group from the Faculty of Physics, University of Warsaw (FUW), have just shown that one of the most spectacular quantum phenomena — that of tunneling — takes place even at temperatures above the boiling point of water. However, what is particularly surprising is the fact that the observed effect applies to hydrogen nuclei, which tunnel in particles floating in solution. The results of measurements leave no doubt: in the studied system, in conditions typical for our environment, tunneling turns out to be the main factor responsible for the chemical reaction!

Continue reading “Exotic quantum effects can govern the chemistry around us” »

Quicker time to discovery. That’s what scientists focused on quantum chemistry are looking for. According to Bert de Jong, Computational Chemistry, Materials and Climate Group Lead, Computational Research Division, Lawrence Berkeley National Lab (LBNL), “I’m a computational chemist working extensively with experimentalists doing interdisciplinary research. To shorten time to scientific discovery, I need to be able to run simulations at near-real-time, or at least overnight, to drive or guide the next experiments.” Changes must be made in the HPC software used in quantum chemistry research to take advantage of advanced HPC systems to meet the research needs of scientists both today and in the future.

NWChem is a widely used open source software computational chemistry package that includes both quantum chemical and molecular dynamics functionality. The NWChem project started around the mid-1990s, and the code was designed from the beginning to take advantage of parallel computer systems. NWChem is actively developed by a consortium of developers and maintained by the Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific Northwest National Laboratory (PNNL) in Washington State. NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

“Rapid evolution of the computational hardware also requires significant effort geared toward the modernization of the code to meet current research needs,” states Karol Kowalski, Capability Lead for NWChem Development at PNNL.

Continue reading “Modified NWChem Code Utilizes Supercomputer Parallelization” »

Last summer, the team reported another achievement: the development of a DNA nanosensor that can measure the physiological concentration of chloride with a high degree of accuracy.

“Yamuna Krishnan is one of the leading practitioners of biologically oriented DNA nanotechnology,” said Nadrian Seeman, the father of the field and the Margaret and Herman Sokol Professor of Chemistry at New York University. “These types of intracellular sensors are unique to my knowledge, and represent a major advance for the field of DNA nanotechnology.”

Chloride sensor

Continue reading “DNA Devices Perform Bio-Analytical Chemistry Inside Live Cells” »

Interesting — DNA Microchips to be released soon.

Researchers presented this incredible work at the national meeting and exposition of the American Chemical Society (ACS) in San Diego, California, on Sunday.

Adam T Woolley, professor of chemistry at Brigham Young University (BYU) said that they are planning to use DNA’s small size and base-pairing capabilities and ability to self-assemble, and direct it to make nanoscale structures that could be used for electronics.

Continue reading “Get ready for DNA-based computer chips!” »

Could a cheap molecule used to disinfect swimming pools provide the key to creating a new form of DNA nanomaterials?

Cyanuric acid is commonly used to stabilize chlorine in backyard pools; it binds to free chlorine and releases it slowly in the water. But researchers at McGill University have now discovered that this same small, inexpensive molecule can also be used to coax DNA into forming a brand new structure: instead of forming the familiar double helix, DNA’s nucleobases — which normally form rungs in the DNA ladder — associate with cyanuric acid molecules to form a triple helix.

Read More ON Mcgill University

Continue reading “Researchers create new triple helix structure for DNA — Many potential uses in chemistry, tissue engineering, etc” »

Life’s chemistry, it appears, is quite kludgy. Such computer metaphors help explain Dr. Venter’s perspective on synthetic biology. Is a genomic version of Moore’s Law in the offing?

Digital CMOS camera with QE technology with improved photon detection capabilities — now this should interest to many medical departments, researchers, and even for security checkpoint screening.

Hamamatsu Corporation has again raised the bar in scientific CMOS camera performance with the 2016 version of the ORCA-Flash4.0 V2. The increased quantum efficiency (QE), now at a peak of 82%, increases the likelihood of detecting the faintest of signals, helping to answer the question “Is it there?” And, for brighter samples, higher QE translates into shorter exposure times without sacrificing image quality. The ORCA-Flash4.0 V2 opens up new possibilities for imaging in low conditions and improves signal to noise at all light levels.

Since its introduction and evolution, the ORCA-Flash4.0 series has become the favorite scientific CMOS camera of investigators everywhere, powering cutting-edge imaging research in every field from biology and chemistry to astrophysics and nanotechnology. The widespread appeal is due to the vast array of high-performance features: low read noise, large field of view, high dynamic range and fast frame rates. The newly enhanced QE of the “Flash V2” only serves to increase the power and versatility of this game-changing camera.

Continue reading “Digital CMOS Camera Series Boosts Quantum Efficiency (QE) For Breakthrough Photon Detection Capability” »