Category Archives: Human Genetic Engineering

Featured Article Academic Journal Main Category: Genetics Also Included In: IT / Internet / E-mail;Medical Devices / Diagnostics Article Date: 29 May 2012 - 11:00 PDT

Current ratings for: 'People's Geographic Origins Traceable With New Genetic Method'

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The team, from the University of California - Los Angeles (UCLA) Henry Samueli School of Engineering and Applied Science, UCLA's Department of Ecology and Evolutionary Biology, and Tel Aviv University, write about their work in a paper published online in Nature Genetics on 20 May.

The researchers hope their method, which they call "spatial ancestry analysis" or SPA, will increase understanding of genetic diversity among populations, which in turn helps us better understand human disease and evolution.

Research areas that may benefit from the new method include finding links between genetic variants and disease and locating parts of genomes that have been subject to positive selection.

SPA is a software tool for analyzing spatial structure in genetic data. It models genotypes in two- and three-dimensional space.

With SPA researchers can model the spatial distributon of each genetic variant. And in this study, the team showed that particular frequency patterns of spatial distribution of gene variants are tied to particular geographic locations.

For genetic variants the team used SNPs ("snips", short for single-nucleotide polymorphisms) from various parts of the genome, including "the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B".

An SNP is a DNA sequence variation where there is a single nucleotide (A, T, C or G) difference in the "spelling" of the sequence.

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People's Geographic Origins Traceable With New Genetic Method

I was at a conference in Venice a few weeks ago on "Evolution in the Age of Genomics." The most interesting presentation at the meeting was by Peter and Rosemary Grant, Princeton biologists who have been studying Darwin's finches in the Galapagos for the past three-plus decades. This work is all the more important because these birds, especially their beaks, have been the poster children of Darwinian evolution for a century and a half.

While most population biology is highly theoretical and conjectural, the Grants have been following what has actually been going on in the wild. Theirs is an exciting scientific and human story, including raising and educating their daughters in a tent while making field observations.

What the Grants emphasized, among many fascinating observations, was the major role hybridization and introgression between distinct "species" played in producing genetic variability in the wild populations. (Introgression means the introduction of part of the genome from a distinct species.)

Whenever there was high inherited variability in a particular population, examination of the DNA indicated that it arose from introgression from a different species. The Grants also described the formation of what would be classed as a new finch species resulting from the full hybridization of two distinct species.

In the discussion session following their joint presentation, someone asked why more attention had not been paid to these inter-species genome transfer events. Peter Grant answered, "Ernst Mayr". What Peter meant was the influence of Mayr's theoretical dictum that recently separated species did not interbreed.

Since Mayr was one of the neo-Darwinian giants of the Modern Synthesis, his speculations were taken as accepted fact. The answer prompted someone in the audience to comment, "Great biologists can only impede progress, not stimulate it."

While interspecific hybridization is now widely accepted in plant evolutionary biology, neo-Darwinian theorists like Jerry Coyne continue to minimize its importance in animals: "Polyploidy is a rapid form of evolution and speciation, one that is fairly common in plants, but very rare in animals. (The reason for its rarity in animals isn't understood, but we discuss the theories in the book I wrote with Allen Orr, Speciation."

Examples of introgression and interspecific hybridization in many different animals are accumulating. Documentation of these processes is aided, as in the Grants' studies, by the application of forensic DNA methods to determine the origins of various genome components. Using the same kind of "microsatellite" markers as in criminal investigations, field biologists can use small tissue samples from wild organisms to pinpoint the sources of DNA regions in their genomes.

A recent paper in Nature, "Butterfly genome reveals promiscuous exchange of mimicry adaptations among species" by The Heliconius Genome Consortium describes the role that interspecific DNA transfers play in the evolution of mimetic wing patterns in butterflies. Similar cases have recently been documented in rodents, newts, and flatfishes. It is likely that interspecific hybridization is far more common in animals than commonly believed.

The reason I was particularly interested in the Grants' observations was that they exemplified an overlooked aspect of population behavior that is relevant to natural genetic engineering. Introgression is a form of horizontal DNA transfer, and interspecific hybridization is one of the most important triggers of large-scale genome restructuring by natural genetic engineering. We are beginning to understand the molecular basis of this triggering because interspecific hybridization is also a destabilizing event for the epigenetic controls that regulate natural genetic engineering functions.

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James A. Shapiro: Interspecific Hybridization and Introgression in Animal Evolution

Sections of living DNA glow red or green to store computer data Could be used like computers inside the body DNA storage can be written, rewritten and erased at will 'Took us three years and 750 attempts,' says lead researcher

By Rob Waugh

PUBLISHED: 10:33 EST, 22 May 2012 | UPDATED: 02:48 EST, 23 May 2012

The idea of storing information in living cells has been the plot of sci-fi fantasies such as Johnny Mnemonic, starring Keanu Reeves - and today it has become reality

It sounds like the stuff of science fiction fantasies, but scientists have turned living cells into data storage devices - like 'living hard drives'.

The idea of storing computer information inside living cells - or human brains - has formed the plot of sci fi thrillers such as Johnny Mnemonic (pictured).

But in reality, the cells are likely to become a method for retrieving information from inside the human body.

The information - stored in the DNA code - can be rewritten and erased at will, so could be used to study ageing cells, and even 'turn off' cells before they turn cancerous.

The cells would be like tiny computers that can 'live' with the body - and could be an incredibly important tool for both computing and medicine.

It took us three years and 750 tries to make it work, but we finally did it, said Jerome Bonnet, PhD, of his latest research, a method for repeatedly encoding, storing and erasing digital data within the DNA of living cells.

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Sci-fi becomes reality as DNA is turned into living drive able to store, read and erase data

Darpa's "Living Foundries" program is looking to "transform biology into an engineering practice." Photo: VA

The military-industrial complex just got a little bit livelier. Quite literally.

Thats because Darpa, the Pentagons far-out research arm, has kicked off a program designed to take the conventions of manufacturing and apply them to living cells. Think of it like an assembly line, but one that would churn out modified biological matter man-made organisms instead of cars or computer parts.

The program, called Living Foundries, was firstannounced by the agency last year. Now, Darpas handed outseven research awardsworth $15.5 million to six different companies and institutions. Among them are several Darpa favorites, including the University of Texas at Austin and the California Institute of Technology. Two contracts were also issued to the J. Craig Venter Institute. Dr. Venter is something of a biology superstar: He was among the first scientists to sequence a human genome, and his institute was, in 2010, the first to create a cell withentirely synthetic genome.

Living Foundries aspires to turn the slow, messy process of genetic engineering into a streamlined and standardized one. Of course, the field is already a burgeoning one: Scientists have tweaked cells in order to developrenewable petroleumandspider silkthats tough as steel. And a host of companies areinvestigatingthe pharmaceutical and agricultural promise lurking with some tinkering, of course inside living cells.

But those breakthroughs, while exciting, have also been time-consuming and expensive.As Darpa notes, even the most cutting-edge synthetic biology projects often take 7+ years and tens to hundreds of millions of dollars to complete. Venters synthetic cell project, for example,costan estimated $40 million.

Synthetic biology, as Darpa notes, has the potential to yield new materials, novel capabilities, fuel and medicines everything from fuels to solar cells to vaccines could be produced by engineering different living cells. But the agency isnt content to wait seven years for each new innovation. In fact, they want the capability for on-demand production of whatever bio-product suits the militarys immediate needs.

To do it, Darpa will need to revamp the process of bio-engineering from the initial design of a new material, to its construction, to its subsequent efficacy evaluation. The starting point, and one that agency-funded researchers will have to create, is a library of modular genetic parts: Standardized biological units that can be assembled in different ways like LEGO to create different materials.

Once that library is created, the agency wants researchers to come up with a set of parts, regulators, devices and circuits that can reliably yield various genetic systems. After that, theyll also need test platforms to quickly evaluate new bio-materials. Think of it as a biological assembly line: Products are designed, pieced together using standardized tools and techniques, and then tested for efficacy.

The process, once established, ought to massively accelerate the pace of bio-engineering and cut costs. The agencys asking researchers to compress the biological design-build-test cycle by at least 10X in both time and cost, while also increasing the complexity of systems that can be designed and executed.

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Darpa, Venter Launch Assembly Line for Genetic Engineering

ScienceDaily (May 16, 2012) Microscopes provide valuable insights in the structure and dynamics of cells, in particular when the latter remain in their natural environment. However, this is very difficult especially for higher organisms. Researchers of Karlsruhe Institute of Technology (KIT), the Max Planck Institute for Polymer Research, Mainz, and the American National Institutes of Health (NIH) have now developed a new method to visualize cell structures of an eighth of a micrometer in size in living fish larvae.

It is published in Nature Methods.

"The zebrafish is perfectly suited for genetic studies of cells, as its larvae are completely transparent," explains Marina Mione, KIT. To visualize certain structures, these are colored mostly by genetic engineering methods using a fluorescent dye. Mione studied parts of the cellular skeleton of fish, the so-called microtubuli. The thread-shaped microtubuli have a length of about 100 m and a diameter of about 20 nm, corresponding to a hundred thousandth of a human hair. "Microtubuli exist everywhere in the cell and are required for its division and motion."

In the new microscopy method, the object is not illuminated completely, but only at a certain spot with special light. Scattered light is minimized and the illuminated detail is represented sharply. A series of images taken at variable illumination is then processed by a computer. In this way, an overall image is obtained. Smart illumination even allows to adjust the depth of field, to image various depth levels, and to combine them into a three-dimensional image on the computer. "Meanwhile, it is possible to reach resolutions of 145 nm in the plane and 400 nm in-between," says Marina Mione. The images are taken within a few seconds, such that movement of the cells does not cause any blurring.

Based on a series of images, videos of the movement of the microtubuli are obtained. In the experiment, it was observed over a period of 60 minutes how the early stage of the fish's lateral line develops about 45 m below the skin of the fish. Via this organ, the fish perceives movement stimuli in water. Such images of living organisms also provide valuable findings regarding the development of vertebrates on the cellular level.

The tropical zebrafish living in freshwater has several advantages as a genetic model organism. It is sufficiently small for easy cultivation and large enough to easily distinguish individual organs. It has a short generation cycle and produces many offspring. As a vertebrate, it has a number of microbiological properties in common with human beings.

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The above story is reprinted from materials provided by Helmholtz Association of German Research Centres, via AlphaGalileo.

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Microscope looks into cells of living fish

Viruses act as tiny piezoelectric generators

Viruses, tiny chunks of protein and nucleic acid, have long plagued mankind and its evolutionary ancestors before it. But thanks to the wonders of modern genetic engineering, researchers believe they have finally been able to instill a beneficial purpose in these deadly pests.

I. From Pest to Power

A team of researchers at Lawrence Berkeley National Laboratory -- one of 16 U.S. Department of Energy (DOE) national laboratories -- has created a special breed of virus that undergoes self-nanoassembly to form tiny piezoelectric generators -- machines which harvest mechanical energy (vibrations or pressure) to directly produce electricity.

The special "bug" is the M13 bacteriophage, a rod-shaped virus that only infects bacteria (such asE. coli bacteria)-- not humans.

Faculty researchersSeung-Wuk Lee, Ramamoorthy Ramesh, and Byung Yang Lee selected the virus due to its tendency to self-assemble into nanofilms, given its rod-like shape. The viruses tightly pack "like chopsticks in a box" and are easy to grow by the millions given a small supply of host bacteria.

II. Refining the Virus

But the effect was too weak to be of use. So the researchers spliced a quadruplet of negatively charged amino acids into one of the coat proteins. The results was a larger voltage gradient across the coat. The researchers also tested stacking films of the modifed viruses to see how thick they could layer the viruses in order to get the maximum effect.

When pressure was applied to the film a 400 millivolt, 6 nanoampere current was put off. That's about a quarter of the voltage of an AAA battery, albeit at a far smaller current. Still it was enough to power a '1' to show up on a low-power liquid crystal display.

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Berkeley Trains "Harmless" Viruses to Harvest Human Kinetic Energy