Genetics Archives

Foldscope Update: Get a Free Microscope for Your Nifty Project Idea

Foldscope Foldscope Update: Get a Free Microscope for Your Nifty Project Idea

Following up on our story from earlier this week about new microscopes that cost less than a dollar to produce, the research team behind the project is now offering free microscopes to citizen-scientists around the world that send in short proposals of what they’re planning to do with them. Offering sub-micron resolution in a package weighing less than ten grams, these microscopes can be boldly taken where no microscope has been before.

foldscope sample Foldscope Update: Get a Free Microscope for Your Nifty Project Idea

The goal is to get 10,000 citizen-scientists to test the microscopes in a variety of settings and to create a “biology/microscopy field manual” using the data gathered by the volunteers.

From the project page:

With support from Moore Foundation, we are currently starting a large scale experiment in hands-on science education called “Ten Thousand Microscope Project.” We intend to enlist 10,000 individuals who would be willing to beta-test Foldscope over the summer and develop single page science experiments, protocols, queries, questions, applications based on using Foldscope in a specific community. We aim to collectively write a crowd-sourced biology microscopy manual with examples collected from scientists, teachers, tinkerers, thinkers, hackers, kids and alike.

Flashback: 50 Cent Origami Microscope for Third-World Diagnostics…

Link: Foldscope: Microscopy for everyone

(hat tip: Scope Blog)

50 Cent Origami Microscope for Third-World Diagnostics

50 Cent Origami Microscope for Third-World Diagnostics

No, Curtis James Jackson III didn’t decide to invest in science and sponsor a microscope. It’s an actual microscope that costs around $0.50 USD to produce ($1 for higher magnification), and can be assembled in under 10 minutes. The Foldscope, developed by the Prakash Lab at Stanford University, provides over 2,000X magnification with submicron resolution, weighs 8.8 grams, fits in a pocket, is battery-powered for up to 50 hours on a single button cell, and is rugged enough to withstand being dropped from three stories or being stomped on by a mad scientist’s boot.

Once assembled, the Foldscope is operated by inserting a standard microscope glass slide, turning on the LED, and viewing while panning and focusing with one’s thumbs. The microscope components are versatile and each can be designed to perform a single microscopy technique, such as brightfield, darkfield, fluoroscopy, or lens-array. Cheap manufacturing costs could allow for labs around the world, especially in developing countries, to have drawers full of Foldscopes, each for carrying out a unique diagnostic test.

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Interview with Dr. Szilard Voros, CEO and Co-Founder of Global Genomics Group

Interview with Dr. Szilard Voros, CEO and Co-Founder of Global Genomics Group

Dr. Szilard Voros, CEO and co-founder of Global Genomics Group (G3), is currently heading the international GLOBAL study, which will enroll up to 10,000 patients with coronary artery disease. The coronary atherosclerotic disease of each patient will be precisely phenotyped with advanced CT angiography; subsequently, each patient’s blood sample will undergo a panomic analysis that includes genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, lipoprotein and proteomics. The trillions of data points collected from the phenotyping and the panomic analyses will be analyzed with specially designed bioinformatics techniques to identify novel pathways and factors contributing to atherosclerosis. We had a chance to speak with Dr. Voros about the project and what led to its development.

Tom Fowler, Medgadget: Dr. Voros, you have an impressive background in your work doing cardiology research. Can you share a unique project you enjoyed being a part of in the past?

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KS-Detect: PCR Driven by Sunlight for Cancer Detection

KS-Detect: PCR Driven by Sunlight for Cancer Detection

PCR (polymerase chain reaction) machines are used to amplify small amounts of DNA into billions of copies. This process can be used to detect the presence of genetic mutations, or of foreign DNA, such as from viruses or bacteria. For the reaction, a number of steps are repeated in a thermal cycle to increase the DNA to a detectable amount. Temperatures typically need to cycle between 50-98ºC (122-208ºF), which has traditionally been achieved with precision electronic resistive heating elements.

Researchers at the Cornell University have developed a solar-powered PCR device, called the KS-Detect, that instead uses a lens to harness sunlight as a heat source (similar to how you might have burned ants with a magnifying glass as a kid). The DNA samples are moved in and out of the light hotspot during cycling to control the temperature. When the cycles are done, a typical PCR dye called SYBR Green is added to the amplified DNA. The dye glows green under UV light if the test is positive for the sequence in interest. A smartphone is then used to take a photo of the glowing sample to analyze and determine the results.

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Beagle Sniffs Out 240 Genomes in Two Days

Beagle Sniffs Out 240 Genomes in Two Days

Whole genome sequencing holds great potential for enriching diagnoses and understanding hereditary risk factors for specific diseases. However, the sheer volume of data involved poses major technical challenges, which limits the utility of this approach. For this reason many clinical geneticists have turned to exome sequencing which looks at a small portion of the genome that codes for proteins.

A team from the University of Chicago have managed to turn the spotlight back on whole genome sequencing by analyzing 240 full genomes in two days by recruiting the computational muscle of Beagle, one of the world’s fastest supercomputers. Beagle is a Cray XE6 supercomputer at the Argonne National Laboratory outside Chicago, and is used for computation, simulation, and data analysis for the biomedical research community.

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Digital Holographic Microscopy for 3D Movies of Swimming Sperm (VIDEO)

Digital Holographic Microscopy for 3D Movies of Swimming Sperm (VIDEO)

Selecting viable sperm for IVF treatment involves looking through a microscope at how the little buggers zip around a Petri dish, but the view is two-dimensional and doesn’t reveal the details of the sperm’s motion. Now a new method has been developed by an international team of researchers that tracks the movement and shape of the sperm cells in 3D and displays the visualization in real-time.

The technique relies on splitting a laser beam into two, sending one through the dish containing the sperm, magnifying it, and then reuniting it with the second half of the beam. The resulting interference between the beam halves creates a hologram that displays the shape and motion. Here’s a quick video of the system showing its live tracking abilities:

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$1,000 Human Genome Sequencing Now Possible Thanks to Illumina’s HiSeq X Scanners

$1,000 Human Genome Sequencing Now Possible Thanks to Illumina's HiSeq X Scanners

DNA sequencing is generally an expensive business and all sorts of methods have been developed to try to bring the cost down. Illumina, a company out of San Diego, California, now claims to be the first to offer machines capable of sequencing human DNA for under $1,000 a pop. For reference, five years ago that figure was about $60,000.

The HiSeq X Ten package from Illumina includes, as the name implies, ten or more HiSeq X sequencers and is aimed at large, high-throughput labs that can benefit from economies of scale. Each of sequencers can process as many as 600 gigabases (Gb) per day of sequencing data, allowing for tens of thousands of genomes to be scanned per year.

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Light-Guiding Hydrogel Brings Optogenetics Closer to Clinical Application

Light-Guiding Hydrogel Brings Optogenetics Closer to Clinical Application

Optogenetics is a promising new field of research that may lead to new treatment options for a variety of conditions. At its root, optogenetics involves introducing optically sensitive cells into an animal that produce desired proteins in response to light stimulation. While the possibilities of this technology are nearly endless, a major hurdle in making it practical is being able to deliver light to the cells, since usually tissue is in the way. Now researchers at Massachusetts General Hospital report developing a new hydrogel implant that can be used to both shine light and sense its presence deep within the body.

The light-guiding hydrogel provides a foundation for cellular growth and can be used to ferry in the genetically engineered cells as well during implantation. To demonstrate the scaffold’s potential for regulating internal body chemistry, the team implanted the device into mice and were able to control the release of  glucagon-like peptide-1 (GLP-1), a protein involved in glucose metabolism, using externally delivered blue light.

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Biosafe Launches Smart-Max System for Stem Cell Processing

Biosafe Launches Smart-Max System for Stem Cell Processing

Biosafe, a company headquartered in Switzerland that manufactures processing technologies for stem cell banking and regenerative medicine, has launched its newest cell processing system called Smart-Max. The fully automated Smart-Max system, which has a touch screen interface, can be used for cell mixing, cooling, thawing, dilution, incubation and digestion. The Smart-Max system is used in tandem with the recently launched Sepax 2 system that can efficiently process umbilical cord blood, bone marrow, peripheral blood or any other blood-like material.

The two systems together offer full automation of all cell processing steps ranging from storage to cell transplant preparation. The device, which can handle cell bags of various sizes for processing, is seen as the final addition to Biosafe’s Coolmix family of devices.

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