ReproCELL Launches Alzheimer's Disease Model Based on iPS-derived Human Neuronal Cells

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YOKOHAMA, Japan, June 7, 2012 /PRNewswire/ --

ReproCELL, Inc. (CEO:Chikafumi Yokoyama PhD) announces today that the company will start commercializing human iPS-derived neurons in which an Alzheimer's disease related gene has been incorporated.

ReproCELL's scientists have successfully incorporated a gene related to Alzheimer's disease using homologous recombinant genetic engineering technology into undifferentiated human iPS cells and then differentiated them into neurons. In these cells, it has been confirmed that amyloid beta 42 is accumulated at higher levels compared to normal neurons. This phenomena is similar to what is observed in neurons of Alzheimer's patients. Accordingly, ReproCELL's scientists believe the newly developed iPS cells can be useful for drug screening to identify new therapeutic molecules to treat Alzheimer's disease patients.

The company will start marketing the cells on June 13th, 2012.

Details of data of the cells will be announced at the 10th annual meeting of ISSCR (International Society for Stem Cell Research) at Yokohama, Japan (June 13th-16th, 2012).

ReproCELL is a world-leading pioneer in commercializing human pluripotent stem cells as an effective tool for drug discovery and development. The company has successfully launched iPS-derived cardiomyocytes for cardiac toxicity testing, followed by the launch of iPS-derived dopaminergic neurons and hepatocytes for efficacy and toxicity screening of drug candidates.

This is the fourth product of the company using iPS technology and the first cellular disease model incorporating a disease-related gene.

Contact: info_en@reprocell.com Tel: 81-(0)45-475-3887 KDX Shin-Yokohama 381 bldg. 8F, 3-8-11 Shin-Yokohama, Kohoku-ku, Yokohama, Kanagawa 222-0033, Japan

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The 25th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems

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*In computer science, people come up with some metaphysical beach-head like artificial intelligence, and they sort of ooze over toward it all astral and handwave-y, and they they actually start coding. Then all kinds of weird boneless crude amphibian code-forms come gasping out of the surf and die on dry land.

IEA-AIE 2012 Event Full Name: Twenty Fifth International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems Date: Sat, 06/09/2012 (All day) to Tue, 06/12/2012 (All day) Where: Dalian China Deadline: Fri, 11/11/2011 (All day)

Topics (((these are great))):

Adaptive Control Expert Systems Machine Learning Application to Design (((Im never gonna believe in a Designer Artificial Intelligence unless it designed its own interfaces and tidied away all its loose wiring))) Financial Applications (((Gosh thanks a lot))) Meta-heuristics Applications to Manufacturing Genetic Programming Model-based Reasoning Autonomous Agents (((Whats that helicopter rotor sound Im hearing Wait, were those gunshots?))) Heuristic Search Multi-Agent Systems Bio-informatics (((Ive got your Turing Machine right here in this Petri dish))) Human Robot Interaction (((Hey look, my new land-mine has Siri built in))) Natural Language Processing Case-based Reasoning (((In case someone mentions Teilhard de Chardin, you can GO TO the next paper))) Integration Systems for Real Life Applications (((Gimme $0.99))) Neural Networks Chance Discovery Intelligence (((Screw-Around Hermeneutics in Websurfing Class))) Intelligent Interfaces Reasoning under Uncertainty (((Am I in the right seminar?))) Computer Vision Intelligent Systems Social Networks Applications Constraint Satisfaction (((A big hit among the marriage-therapist user community))) Intelligent Systems in Education Soft Computing Conversational Informatics Internet Applications Spatial Reasoning Data Mining Interaction Planning and Scheduling Speech Recognition System Decision Support Systems KBS Methodology Temporal Reasoning Distributed Problem Solving Knowledge Management Evolutionary Algorithms Knowledge Processing

http://ssdut.dlut.edu.cn/iea-aie/webpages/index.htm

The 25th International Conference on Industrial, Engineering &

Other Applications of Applied Intelligent Systems

2012 Dalian, China

Sponsor:International Society of Applied Intelligence (ISAI)

Organized in cooperation with:

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The 25th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems

Councils protect their growers from Genetic Engineering

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7 June 2012

Councils protect their growers from GE

In the vacuum of inaction left by the National Government, local councils are having to lead the way in keeping New Zealand free of genetic engineering, the Green Party said today.

Hastings District Council have given official support to the GE free movement, voting unanimously in support of a proposal to declare the district GE free.

This is an exciting move made by the Hastings District Council but they have been forced to take this action because the National Government is refusing to, said the Green Party GE spokesperson Steffan Browning.

This region by region approach will be able to protect some growers but is not the real solution New Zealand needs.

The growers in the Hawkes Bay have identified that they need to be able to reap the significant branding benefits of being able to market GE free food, said Mr Browning.

These producers are receiving demand for GE free products and we need to be protecting their market for them

There are not sufficient liability protections for non GE growers should their produce get contaminated.

Farmers in Australia are already experiencing loss of income due to contamination by GE crops.

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Councils protect their growers from Genetic Engineering

James A. Shapiro: Can Cells Bias Natural Genetic Engineering Toward Useful Evolutionary Outcomes?

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A few blogs ago I asked, "Where, in fact, do 'the good ones' really come from?" By "good ones" I meant useful genome changes in evolution. This question stimulated some debate about whether it was possible to distinguish good changes from bad changes before they occur.

In the abstract, this may seem an overwhelmingly difficult problem. But if we think a bit about the highly organized state of the genome and non-random natural genetic engineering, biasing changes toward "good ones" becomes more conceivable.

I have already discussed purposeful, targeted changes in the immune system. The immune system illustrates how efficiently cells can target DNA restructuring by recognizing specific sequences and coupling DNA changes to transcription (copying DNA sequence into RNA).

Some evolutionists object that a somatic process like antibody synthesis provides no model for germline changes in evolution. So let's examine natural genetic engineering events in microbial cells. We'll look at mobile genetic elements targeted in ways that increase their evolutionary potential.

Mobile genetic elements come in many forms. Some operate purely as DNA. Others make an RNA copy and reverse transcribe it back into DNA as it inserts at a new location. Elements that move, or transpose, to multiple new locations are called "transposons" or "retrotransposons" (if they use an RNA intermediate).

Other mobile elements only insert in particular locations by a process called "site-specific" recombination. In bacterial evolution, this process is used in specialized structures called "integrons" that capture casettes containing protein coding sequences for antibiotic resistance, pathogenicity, and other functions.

What all mobile elements share are proteins that aid them to cut and splice DNA chains so that they can construct novel sequences, much as human genetic engineers do in their test tubes. These proteins have various names, such as "recombinase," "transposase," and "integrase." It is the specificity of the cutting reactions involving these proteins that determines where a mobile element moves in the genome.

One fascinating case of highly biased integration is the bacterial transposon Tn7. Tn7 has two specialized proteins to target its transposition. The TnsD protein directs Tn7 to insert into a special "attTn7" site in the chromosomes of many bacterial species where it does not disrupt any host functions and so causes no deleterious effects.

Another, more interesting protein, TnsE, directs Tn7 to insert into replicating DNA molecules. The reason this is important is that transmissible plasmids replicate their DNA as they transfer from one cell to another. TnsE targeting to plasmids in transit to new cells thus enhances the spread of Tn7 and the resistances it carries to many different kinds of bacteria.

Tn7 carries its antibiotic resistance determinants in an integron. Integrons and their recombinase proteins are likewise specialized to participate in plasmid spreading through bacterial populations. Plasmids enter new cells as single-stranded DNA. We learned just in 2005 that integron site-specific recombinases are special in operating on single-stranded DNA, not double-stranded molecules like previously studied recombinases. Moreover, integron recombinase synthesis is triggered by the entrance of single-stranded DNA into a cell. So integron activity is intimately linked in more than one way to plasmid transfer.

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James A. Shapiro: Can Cells Bias Natural Genetic Engineering Toward Useful Evolutionary Outcomes?

‘Wormhole’ looks at race

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A flickering beacon of science and reason amid cables superstitious Dark Ages, Through the Wormhole With Morgan Freeman (9 p.m., Science) returns for a new season with its most controversial episode.

Is There a Superior Race? goes right to the heart of one of mankinds most vexing and flammable notions. The mapping of the human genome at the end of the 20th century was thought to have put an end to the idea of race. Since all humans share virtually identical genetic material, differences were dismissed as merely skin deep.

But over the past 10 years, a few scientists have begun to explore some of the genetic differences between racial groups, particularly those mutations that occurred during the past 20,000 years roughly the span of human history.

Charles Darwin theorized that once human beings formed civilizations, they would no longer mutate or evolve. But scientists have found an astounding number of recent genetic mutations that are clearly responsible for racial differences that transcend skin tone or bone structure.

Europeans have been raising livestock for dairy products for only a few thousand years, yet in that relatively short span they have developed genes that enable them to digest cows and goats milk. These genes are noticeably lacking in people from Asia, where widespread dairy agriculture never took hold. But its a perilous leap from genetic differences in human digestion to theorizing that some races have evolved to become smarter than others.

One pessimist suggests that genetic engineering may enable a handful of people to breed a stronger, disease-resistant race that could dominate the poorer multitudes, leaving them to reproduce the old-fashioned way.

Another theorist suggests that the evolution of the human mind may no longer be taking place in our brains or in our genes, but in our hivelike adaptation of social media. He envisions a future where billions of people linked by technology could solve problems together and advance humanity in ways we cant even imagine now.

Tonights other highlights

A new baby irks a pampered bulldog on Dogs in the City (7 p.m., CBS).

Toby Keith and Kristen Bell host the 2012 CMT Music Awards (7 p.m.).

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‘Wormhole’ looks at race

Camel Pharmacies?

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Researchers create transgenic cells that may help camels produce milk full of therapeutic proteins.

By Hayley Dunning | June 4, 2012

Camels highly adaptable nature and resistance to disease has always made them essential to desert-dwelling cultures, and with a little help from genetic engineering they may one day provide us with cheaper drugs. A team of researchers at Dubais Camel Reproduction Centre have created transgenic camel embryos to which they introduced non-human genes similar to those of humans, according to United Arab Emirates newspaper, The National. They havent yet been able to introduce human genes into the embryos, but the head of the Centres reproductive biology lab, Nisar Wani, told The National that he and his team have taken an important first step. If human genes that code for proteins such as insulin could be added, the camels could produce milk laden with pharmaceuticals to fight diabetes, obesity and emphysema.

Patients with genetic disorders need these proteins, which are very costly today because companies are producing them by bacterial cultures in their labs, Dr Wani said. But if were successful at producing them in the milk, say in 15 to 30 litres, we can get a huge quantity of protein and that will drastically decrease their cost worldwide.

Wanis group is currently working on increasing the ratio of implanted embryos that survive to delivery, and introducing new genes from other species to improve milk production. Increased lactation could bring the cost of milk-borne drugs down, but Wani cautions that mass-production is still at least five years off.

The Centres success with camels, including sequencing its genome and producing the first cloned camel in 2009, prompted Wani to predict that this new innovation could one day make camels ideal candidates for growing human organs for transplant.

Soon we will have organs that will be like universal tools for anybody who has a kidney failure or heart problems, he said. He can get the organ from the animal.

By Bob Grant

A genetic testing company fields concerns that their latest gene patent goes against their core beliefs regarding access to genetic information.

By Jef Akst

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Camel Pharmacies?

Oragenics and Intrexon Announce Worldwide Exclusive Collaboration for Lantibiotics

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TAMPA, Fla. & GERMANTOWN, Md.--(BUSINESS WIRE)--

Oragenics, Inc. (ORNI) (the Company), a leader in the area of oral care probiotics and a developer of therapeutic products including novel antibiotics, and Intrexon Corporation, a synthetic biology company that utilizes its proprietary technologies to provide control over cellular function, announced today the formation of a global exclusive channel collaboration through which Oragenics intends to develop and commercialize lantibiotics, a novel class of broad spectrum antibiotics, as active pharmaceutical ingredients (API) for the treatment of infectious diseases in humans and companion animals.

John N. Bonfiglio, Ph.D., President and Chief Executive Officer of Oragenics, stated, We are excited about the tremendous potential that the collaboration brings to the Company and we look forward to working with Intrexon. Intrexons state-of-the-art science will allow us access to new techniques and processes which could rapidly allow us to move toward commercializationofthis exciting and novel class of antibiotics.

Randal J. Kirk, CEO and Chairman of the Board of Intrexon, said, Intrexon thrives on accepting challenges and solving problems that have proved resistant to the efforts of its predecessors. As was the case with our recombinant human alpha 1-antitrypsin (rHuA1AT) project, the production of lantibiotics through bioindustrial process has been a high-value goal that we now take on with confidence and commitment. We are pleased to be working with the Oragenics team on this high-value opportunity.

Under the collaboration, Oragenics will utilize Intrexon's advanced transgene and cell engineering platforms for the development and production of lantibiotics, a class of peptide antibiotics that naturally are produced in Gram-positive bacteria and contain the characteristic polycyclic thioether amino acids lanthionine and methyllanthonine. Lantibiotics have shown broad-spectrum antibiotic properties against Gram-positive bacterial infections, such as MRSA and VRE in pre-clinical studies, yet their development as commercially viable products continues to be subject to significant technological hurdles.

Intrexon will be responsible for technology discovery efforts, cell-engineering development, and certain aspects of the manufacturing process. Oragenics will be responsible for conducting preclinical and clinical development of candidate lantibiotics, as well as for other aspects of manufacturing and the commercialization of the product(s).

Under terms of the transaction agreements:

Oragenics will receive an exclusive, worldwide license to utilize the products of Intrexons modular genetic engineering platform for the development of API and drug products involving the direct administration to humans or companion animals of a lantibiotic for the prevention or treatment of infectious disease.

Intrexon will apply its proprietary platforms and technologies, including UltraVector, DNA and RNA MOD engineering, protein engineering, transcription control chemistry, genome engineering, and cell system engineering, to Oragenics lantibiotics program.

Oragenics is responsible for funding the further anticipated development of lantibiotics toward the goal of commercialization.

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Milbank: Before GOP clones Reagan genetic flaws must be fixed

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When news broke a vial of Ronald Reagans blood was being auctioned, the price quickly jumped to $30,000 as websites and blogs explored a tantalizing possibility: Did this mean the late president could be cloned?

Before mad scientists got the chance to perform a Dolly-the-Sheep experiment with the 40th president, the seller succumbed to criticism and decided to donate the blood to the Ronald Reagan Presidential Foundation. But this should only encourage the cloning speculation because the Gippers DNA is now in the hands of those who would most like to reproduce him: Republicans.

Party officials have been making the pilgrimage to the Reagan Library this year to express their wish to re-create the great man. I believe boldness and clarity of the kind that Ronald Reagan displayed in 1980 offer us the greatest opportunity to create a winning coalition in 2012, vice presidential aspirant Paul Ryan said at the library last week.

Also making the trip were VP hopefuls Marco Rubio and Chris Christie. Like Ronald Reagan, I believe in what this country and its citizens can accomplish, the latter declared. The America I speak of is the America Ronald Reagan challenged us to be.

The man they hope to join on the ticket, Mitt Romney, once boasted he was not trying to return to Reagan-Bush. Now he says the partys standard-bearer should be in the same mold as Ronald Reagan.

But before they go filling that mold by mapping the Reagan genome, Republicans may wish to consider some genetic flaws that party scientists should repair in the cloning process. To make the Reagan clone more compatible with todays Republican Party, a bit of genetic engineering may be in order:

AFL-1: Reagans AFL-1 gene, on the labor chromosome, has a mutation that made him susceptible to workers rights. He said of unions: There are few finer examples of participatory democracy. He said the right to join a union is one of the most elemental human rights. And he said collective bargaining played a major role in Americas economic miracle.

EPA-4: Reagans EPA-4 gene, on the regulatory chromosome, has a protein that can summon anti-industry sympathies. He signed a law establishing efficiency standards for electric appliances and an update to the Safe Drinking Water Act punishing states that didnt meet clean-water standards.

SSA-2 and MDCR-1: These related genes, on the long arm of the retirement chromosome, are problematic. Reagan expanded Social Security in 1983 and imposed taxes on wealthy recipients. He also signed what was at the time the largest expansion of Medicare in its history.

DEBT-1, DEBT-2, DEBT-3: A trio of abnormalities on the fiscal chromosome caused Reagan to increase taxes several times after his initial tax cut, to embrace much higher taxes on investments than current rates and to sign 18 increases in the federal debt limit.

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Scripps Research Institute's Richard A. Lerner Wins Prince of Asturias Award for Scientific and Technical Research

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LA JOLLA, Calif., May 31, 2012 /PRNewswire/ --Scripps Research Institute Professor Richard A. Lerner, MD, has won a prestigious international honor, the Prince of Asturias Award for Scientific and Technical Research, according to an announcement made today by the Prince of Asturias Foundation. Lerner shares the award with British biochemist Sir Gregory Winter, PhD.

Sometimes called the "Spanish Nobel Prize," the Prince of Asturias Award for Scientific and Technical Research is bestowed for findings that "represent a significant contribution to the progress and welfare of mankind." Winners receive 50,000 Euros (about $62,000), a diploma, an insignia bearing the foundation's coat of arms, and a sculpture specially created for the awards by the late Spanish artist Joan Miro.

"This honor for Richard is richly deserved," said Scripps Research President and CEO Michael A. Marletta, PhD. "His discoveries have had a very significant impact on the treatment of disease and I am delighted that this recognition has come to him."

"It is my honor to accept this prestigious award together with Sir Greg," said Lerner, "This is a wonderful recognition for the field of immunochemistry and combinatorial antibody libraries and all that they have contributed to human health."

The announcement of the jury was broadcast live from Oviedo, Spain, to more than 150 countries at noon, local time.

The foundation's statement reads, "The researchers Gregory Winter and Richard A. Lerner stand at the forefront of research on the immune system. The advances in the use of antibodies as therapeutic tools have provided new ways of preventing and treating immune disorders, degenerative diseases and different types of tumours. In many cases, the use of antibodies has alleviated the suffering of patients and has halted the progression of the disease. These researchers have managed to create a synthetic immune system in the test tube, as well as demonstrating its preventive and therapeutic potential due to exceeding the natural antibody repertoire the human body can generate."

This work has resulted in two drugs currently on the market, as well as other compounds currently in clinical trials. The drug Humira (adalimumab), marketed by Abbott, provides a treatment for inflammatory diseases such as rheumatoid arthritis, Crohn's disease, and plaque psoriasis. Humira is now reported to be the top selling drug in the world.

Benlysta (belimumab), which was developed by GlaxoSmithKline and Human Genome Sciences, was approved in the United States for the treatment of the most common type of lupusa chronic, life-threatening autoimmune diseasein the spring of last year. At that time, Benlysta became the first new drug for lupus in 50 years.

41 Nominations This year, 41 nominations from Argentina, Bulgaria, Canada, Costa Rica, Cuba, France, Germany, Holland, Israel, Italy, Japan, Mexico, Russia, Sweden, Switzerland, Turkey, United Kingdom, United States and Spain were in the running for the Prince of Asturias Award for Scientific and Technical Research. This prize is the fourth of eight awards bestowed each year by the Prince of Asturias Foundation. The others are in the fields of the arts, communications and humanities, literature, sports, social sciences, international cooperation, and concord (peace).

The Prince of Asturias Foundation was founded in the city of Oviedo on September 24, 1980, at a formal ceremony presided over by His Royal Highness the Prince of Asturias, heir to the throne of Spain, who was accompanied by his parents, Their Majesties the King and Queen of Spain.

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Latest genomic studies shed new light on maize diversity and evolution

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Public release date: 3-Jun-2012 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

June 3, 2012, Shenzhen, China BGI, the world's largest genomics organization, together with other 17 international institutes, announced that they completed the second generation of maize HapMap (Maize HapMap2) and genomics studies on maize domestication and improvement. The two separate studies were published online in the same issue of Nature Genetics.

The studies mark an important milestone in Maize (Zeamays) genomics research, providing an unprecedented glimpse into maize's 'wonderful diversity' and revealing new insights into the evolutionary history of maize genome. These studies will provide valuable insights for botanists and breeders worldwide and facilitate the genetic engineering of this vital cereal crop in the world.

In addition to BGI, the other collaborative organizations include U.S. Department of Agriculture (USDA), Cold Spring Harbor Laboratory, University of California Davis, Cornell University, the International Maize and Wheat Improvement Center (CIMMYT), and others.

Characterizing Maize's Impressive Diversity

Maize's impressive diversity has been attracting much attention in the academic community and agricultural sector. However, characterizing this diversity- in particular at high levels- has been technically challenging. In this study, researchers developed a novel population-genetics scoring model for comprehensively characterizing the genetic variations, including single nucleotide polymorphisms (SNPs), small insertion-deletions, and structural variations (SVs). Through the comprehensive analysis, about 55 million SNPs were identified across 103 inbred lines of wild and domesticated maize. They also found that SVs were prevalent throughout the maize genome and were associated with some important agronomic traits, such as those involved in leaf development and disease resistance.

The researchers also investigated the major factors that influence the maize genome size. The results showed the genome size variations between maize and Gama grass (Tripsacum dactyloides), maize's sister genus, are mostly driven by the abundance of transposable elements (TE). In contrast with the fact that the intra-species genome size variation is influenced by the DNA structure known aschromosomal knobs. In addition to the differences, there is tremendous unity of gene content between maize relatives, suggesting that the adaptations, such as frost and drought tolerance, amongst all of maize's relatives are likely integratable in maize.

Tracing Maize's Evolution and Improvement

Since maize was domesticated approximately 10,000 year ago, its wild progenitor went through a particular transformation that had radically altered maize's wild species to meet human's needs. To comprehensively trace maize's evolution process, researchers sequenced 75 wild, landrace and modern maize lines. Through the comparative population genomics analysis, they found the evidence of new genetic diversity that has arisen since domestication, maybe due to the introgression from wild relatives. They also identified a number of genes that obviously had played important roles in the transition from wild to domesticated maize.

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Latest genomic studies shed new light on maize diversity and evolution

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

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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

People's Geographic Origins Traceable With New Genetic Method

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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

Microscope looks into cells of living fish

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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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Darpa, Venter Launch Assembly Line for Genetic Engineering

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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

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

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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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Reification is alright by me! | Gene Expression

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Long time readers know that Im generally OK with reificationas long as we dont take it too seriously. And we do that all the time. An object is really only an object in a human-sense. Reduced down to particle physics it is an altogether different entity. But on the human-scale asserting that a chair is indeed a chair, rather than cellulose, etc., (or now, polymers), and further down basic macromolecules, is a useful fudge. Similarly, Im generally skeptical of the idea that we have a clear & distinct model for what a species is. The framework is very different when youre talking about prokaryotes, as opposed to plants, as opposed to mammals. The question is not species, but what utility or instrumental value does the category or class species have?

For most of the stuff Im concerned with, the messy shapes of reality which are the purview of biological science, we are all fundamentally nominalists in our metaphysic. We may accept that were idealists in the sense of cognitive or evolutionary psychology, but human intuition does not make it so. The categories and classes we construct are simply the semantic sugar which makes the reality go down easier. They should never get confused for the reality that is, the reality which we perceive but darkly and with biased lenses. The hyper-relativists and subjectivists who are moderately fashionable in some humane studies today are correct to point out that science is a human construction and endeavor. Where they go wrong is that they are often ignorant of the fact that the orderliness of many facets of nature is such that even human ignorance and stupidity can be overcome with adherence to particular methods and institutional checks and balances. The predictive power of modern science, giving rise to modern engineering, is the proof of its validity. No talk or argumentation is needed. Boot up your computer. Drive your car.

All this is to preface my explanation of my post below, Finding Fake Roots. Some readers & commenters were a bit confused or unclear at what I was getting at. Here in a nutshell is the problem as I see it: in Finding Your Roots Henry Louis Gates Jr. shifts back and forth between uniparental phylogenies, more contemporary model clustering assessments of genetic relatedness and relationships, and natural history. The map above illustrates human migrations as they were commonly depicted in the mid-2000s during the peak of uniparental lineages. By uniparental, I mean the direct maternal line, as defined by mtDNA, and the direct paternal line, as defined by Y chromosomes. These two methods were easy to conceive as a phylogentic tree, because thats what these two genomic regions are. Theres no recombination; mixing & matching between parents. You get your Y from your paternal lineage (if you are male), and your mtDNA from your mother. These neat phylogenetic trees of mtDNA and Y chromosomal lineages were then easily transposed to a spatial and temporal scale. Ergo, nice cartographic infographics like the one above.

But all good things come to an end. With SNP chips, which allow researchers to type individuals across hundreds of thousands of markers, we now are at the stage where we can move beyond the direct maternal and paternal lines. Rather than just one line of descent, we get a full picture of ones ancestors. To the left are my daughters result from 23andMe. As I have noted before, Im 99% sure theres a problem with their results for people with particular mixed ancestries (my half East Asian/European friends get good results, so I assume its a reference population problem). She is about 40 percent South Asian on ADMIXTURE, and that makes sense since Im 80-90 percent South Asian (the balance is East Asian, which is not surprising due to my familys origin). But lets put that to the side. What are these results telling us?These algorithms are powerful. But we always need to be very careful about imposing our own frame upon them. They are excellent at gauging genetic relatedness, but they are not so excellent at telling us our history.

To the left is my best guess at my history. Im 80-90% South Asian. Thats pretty clear, and will show up on any clustering algorithm with explicit models. It will also be clear on a PCA, where South Asians can shake out as their own independent dimension. But 10,000 years ago South Asians as we understand them geneticallyprobably did not exist. By probably, Im about 95% sure. The genetic analyses which support this proposition are abstruse, but they make sense of a great deal of other data. The South Asian genetic cluster is a real one, but it is compound formed within the last 10,000 years of two very distinct populations. Just because it is a hybrid does not mean that one should automatically reduce it to its antecedents. Many real populations originate as hybrids. Similarly, I think that there is a high chance that Europeans, as we understand them today, did not exist 10,000 years ago. Rather, modern Europeans as well may be a compound of various populations which expanded demographically, and synthesized with each other, between the end of the Ice Age and history.

In my post below some commenters argued that obviously implausible inferences from a thin set of reference populations are acceptable considering Henry Louis Gates Jrs target audience. But that really wasnt my main point. Rather, it was that he was eliding the distinction between uniparental markers, and the clusters generated by modeled based ancestry assignment algorithms, and ascribing the phylogenies of the former to the latter. It is important to note that categories like Europeans are only approximations. But theyre damn good approximations today! Nevertheless, note the qualification of time: they may have basically no meaning at some point in the recent past. Theyre powerful when it comes to precisely partitioning modern variation, but they dont tell us the history of that variation.

When constructs lead us to a false perception of reality, were using them incorrectly. We shouldnt blame the abstractions. Rather, we should blame humans. Ourselves.

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Evolution and Bible cannot mix

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By Babu G. Ranganathan

Christian leaders across denominations have compromised with Darwinian evolutionary theory, which has caused havoc of faith for millions. Many Christian leaders argue that God used evolution to create all life. This position is neither biblical nor scientific and opens the door for utter ridicule and disrespect. If Darwinian macro-evolutionary theory is true then any belief in God is nothing more than blind faith because God is not necessary for the process.

The Bible teaches that God began with a perfect creation where there was no suffering and death. There was death of plant life but not life possessing "soul" (i.e. animals and humans). There was even perfect peace and harmony between animals. There were no meat-eating animals in the beginning (Genesis 1:30). Animal and human death did not occur until after man sinned. There was no struggle and survival-of-the-fittest among animals or man in the beginning. Man and all creation, which was placed under man, fell to imperfection, struggle, suffering, and death because of the sin of Adam and Eve, mankind's first parents. All this is opposite to what Darwinian macro-evolutionary theory teaches. Unlike the Bible, the theory of evolution teaches the world was never perfect and the animal kingdom always existed with struggle and suffering and death (extinction). Scripture teaches these conditions came into being after the fall of man - not before!

You cannot mix Darwinian macro-evolution and the Bible. To say God used evolution to create man is in direct contradiction to the doctrine of the Fall of Man because the process of evolution involves struggle, pain, suffering, and death. God did not begin with these or with half-evolved fish, amphibians, reptiles, birds, mammals, etc. God created a perfect world with complete, fully-functioning, and fully-formed species from the very beginning (i.e. complete fish, complete amphibians, complete reptiles, complete birds, complete mammals, etc.). How could a partially-evolved species survive anyway? It would be unfit for survival. Survival-of-the-fittest wouldn't allow for partially-evolved species with partially-evolved tissues, organs, and biological functions and structures to survive!

More and more evolutionary scientists are abandoning the theory of gradual macro-evolution and are adopting a new theory, "Punctuated Equilibrium" which teaches that life forms changed suddenly, not gradually, by chance from one kind to another as a result of massive random genetic mutations caused by massive random radiation from the environment.

The reason for this big change among evolutionists is because they realize that species cannot survive in a partially evolved state with incomplete traits, tissues, organs, and body functions. A reptile with scales in the process of turning to feathers would not have the function of either trait.

The problem with punctuated equilibria, however, is that it is contrary to what we know about the nature of mutations and radiation. Punctuated equilibrium is nothing more than blind faith.

In Genesis 1, God says 10 different times that all living things must reproduce after their own "kind," not into other kinds! A dog must reproduce a dog. Different varieties of dogs are possible genetically, but they will all still be dogs and not something else.

God placed within the "kinds" the genetic ability for variation and change to adapt to changing environments, but this is not the same as evolution from one kind into another kind as Darwinian macro-evolutionary theory teaches.

All the biological similarities between species are because of a common Designer (God) Who designed similar functions for similar purposes in all the various forms of life, not because of a common ancestry as evolutionists teach.

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Evolution and Bible cannot mix

Berkeley Trains "Harmless" Viruses to Harvest Human Kinetic Energy

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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

H5N1 Paper Published: Deadly, Transmissible Bird Flu Closer than Thought?

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After an epic debate over whether to release research detailing how scientists created H5N1 in the lab, Nature finally published one of the two controversial papers on Wednesday.

You might not have noticed, but the influenza world has been in a bit of an uproar since late last year, when news leaked out that two teams of researchers had purposefully tweaked H5N1 bird flu in the lab to potentially make it more transmissible among human beings. (H5N1 spreads like wildfire among birds and usually kills them but the virus only rarely seems to jump to human beings, though when it does the infections are often fatal.)

The two scientists Yoshihiro Kawaoka of the University of WisconsinMadison and TIME 100 honoree Ron Fouchier of Erasmus University in the Netherlands had submitted their research toNature andScience, respectively, with the expectation of swift publication. In December, the National Science Advisory Board for Biosecurity (NSABB) did something unprecedented: they ruled that the two papers should be censored if published, that they should be scrubbed of the complete methods and viral mutations that the researchers studied, in order to head off the risk that terror groups could use the information to craft a deadly bioweapon.

(PHOTOS: The Bird Flu Outbreaks in 2008)

That led to intense fighting within the scientific community. Some researchers wanted the papers published in full, both because they believed the work could help arm us against a future flu pandemic, and because they worried about the chill of government censorship on science. Other scientists were against publication and even the experiments themselves, believing that nothing gleaned from the work could be important enough to offset the risk of creating a potentially deadly flu virus.

In the end, Fouchier explained that his man-made flu virus wasnt the merciless killer that early media reports had made it out to be Kawaokas man-made virus was always believed to be less dangerous and in March the NSABB took a look at revised papers submitted by the two research teams and voted to recommend that they be published.

On Wednesday, Nature finally published Kawaokas research. (Were still waiting for the Fouchier paper, though the Dutch scientist was recently granted an export license for his work, so it should appear soon.) The sobering takeaway: avian H5N1 flu viruses in nature may be only one mutation away from spreading effectively between mammals, likely including human beings. If that happens and if H5N1 retains its apparently sky-high mortality rate we could be in for serious trouble.

For all the controversy, the research itself is actually quite fascinating. Kawaoka and his team mutated H5N1s hemagglutinin (HA) gene the H in H5N1 which produces the protein the virus needs to attach itself to host cells. They produced millions of genes, mimicking the effect of random mutation in nature, and found one version of H5N1 hemagglutinin that seems particularly effective at invading human cells.

(MORE: Dangers of Man-Made Bird Flu Are Exaggerated, Its Creators Say)

The genes for that protein contained four new mutations, three of which altered the shape of the gene, while the fourth one changed the pH level at which the protein attaches to the cell and injects the viruss genetic material inside. (Its a bit reminiscent of Alien, if the virus is the face-hugger and this poor guys face is the cell.)The team combined the mutated HA gene with seven other genes flu viruses have eight genes in all from the highly transmissible if not highly deadly H1N1 strain, which caused the 2009 flu pandemic. The result was an H1N1 virus with mutant H5N1 hemagglutinin proteins on the outside.

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H5N1 Paper Published: Deadly, Transmissible Bird Flu Closer than Thought?

Robot Reveals the Inner Workings of Brain Cells

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Newswise Gaining access to the inner workings of a neuron in the living brain offers a wealth of useful information: its patterns of electrical activity, its shape, even a profile of which genes are turned on at a given moment. However, achieving this entry is such a painstaking task that it is considered an art form; it is so difficult to learn that only a small number of labs in the world practice it.

But that could soon change: Researchers at MIT and the Georgia Institute of Technology have developed a way to automate the process of finding and recording information from neurons in the living brain. The researchers have shown that a robotic arm guided by a cell-detecting computer algorithm can identify and record from neurons in the living mouse brain with better accuracy and speed than a human experimenter.

The new automated process eliminates the need for months of training and provides long-sought information about living cells activities. Using this technique, scientists could classify the thousands of different types of cells in the brain, map how they connect to each other, and figure out how diseased cells differ from normal cells.

The project is a collaboration between the labs of Ed Boyden, associate professor of biological engineering and brain and cognitive sciences at MIT, and Craig Forest, an assistant professor in the George W. Woodruff School of Mechanical Engineering at Georgia Tech.

Our team has been interdisciplinary from the beginning, and this has enabled us to bring the principles of precision machine design to bear upon the study of the living brain, Forest says. His graduate student, Suhasa Kodandaramaiah, spent the past two years as a visiting student at MIT, and is the lead author of the study, which appears in the May 6 issue of Nature Methods.

The method could be particularly useful in studying brain disorders such as schizophrenia, Parkinsons disease, autism and epilepsy, Boyden says. In all these cases, a molecular description of a cell that is integrated with [its] electrical and circuit properties has remained elusive, says Boyden, who is a member of MITs Media Lab and McGovern Institute for Brain Research. If we could really describe how diseases change molecules in specific cells within the living brain, it might enable better drug targets to be found.

Automation

Kodandaramaiah, Boyden and Forest set out to automate a 30-year-old technique known as whole-cell patch clamping, which involves bringing a tiny hollow glass pipette in contact with the cell membrane of a neuron, then opening up a small pore in the membrane to record the electrical activity within the cell. This skill usually takes a graduate student or postdoc several months to learn.

Kodandaramaiah spent about four months learning the manual patch-clamp technique, giving him an appreciation for its difficulty. When I got reasonably good at it, I could sense that even though it is an art form, it can be reduced to a set of stereotyped tasks and decisions that could be executed by a robot, he says.

To that end, Kodandaramaiah and his colleagues built a robotic arm that lowers a glass pipette into the brain of an anesthetized mouse with micrometer accuracy. As it moves, the pipette monitors a property called electrical impedance a measure of how difficult it is for electricity to flow out of the pipette. If there are no cells around, electricity flows and impedance is low. When the tip hits a cell, electricity cant flow as well and impedance goes up.

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Robot Reveals the Inner Workings of Brain Cells