Category Archives: Genetic Engineering

CRISPR Cas9: A novel approach to genetic engineering
Provides the basic mechanism behind the CRISPR Cas9 complex, while describing application and need.

By: Walter Wang

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CRISPR Cas9: A novel approach to genetic engineering - Video

CRISPR Webinar by Drs. Barrangon, Zhang and Church
Webinar sponsored by OriGene and held by GEN, Genetic Engineering Biotechnology News This webinar on the genome editing system CRISPR/Cas9 is given by three scientists who have been pioneering...

By: OriGene Technologies Inc.

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CRISPR Webinar by Drs. Barrangon, Zhang and Church - Video

Today, April 25, 2014 is National Arbor Day and a reminder of the importance that individuals and groups need to plant and care for trees. This means ensuring that arboriculturists and foresters have access to the most up to date agricultural technologies. The American Chestnut blight is recent example of how genetic engineering has served as one of these vital technologies.

A recent piece published in Scientific American told of the blight of the American Chestnut nearly wiped out by a fungal disease and efforts to genetically engineer the trees to resist the fungus and reintroduce healthy trees back into America forests. Ferri Jabrs A New Generation of American Chestnut Trees May Redefine Americas Forests examines the history of the American Chestnut going from its role of providing food and shelter for animals and people to nearly becoming obsolete.

Before the early 1900s, one in every four hardwood trees in North Americas eastern forests was an American chestnut, providing copious food and shelter for animals and people alike.

A New York City nurseryman named S. B. Parsons imported Japanese chestnut trees in 1876, which he raised and sold to customers who wanted something a little exotic in their gardens. Other nurseries in New Jersey and California soon did the same.

One or perhaps allof these shipments concealed the pathogenic fungusCryphonectria parasitica, which chokes chestnut trees to death by wedging itself into their trunks and obstructing conduits for water and nutrients. Asian chestnut trees had long evolved resistance toC. parasitica, but their American relativeswhich had never encountered the pathogen beforewere extremely susceptible to the fungal disease known as chestnut blight.

In 1904 the fungus was first discovered in New York State and soon spread to New Jersey, Connecticut, Massachusetts and Pennsylvania. Within 50 years,C. parasitica killednearly four billion chestnut trees.

Since the 1980s several generations of researchers at the State University of New York College of Environmental Science and Forestry (S.U.N.Y.ESF) have toiled to restore the American chestnut to its native habitat. Genetic engineering has offered a successful route to restoration.

By taking genes from wheat, Asian chestnuts, grapes, peppers and other plants and inserting them into American chestnut trees, William Powell of S.U.N.Y.ESF and scores of collaborators have created hundreds of transgenic trees that are almost 100 percent genetically identical wild American chestnut yet immune to C. parasitica.

The scientists hope to get federal approval to begin planting these trees in the forest within the next five years (See The American Chestnuts Genetic Rebirth in the March 2014 issue of Scientific American).

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Remember the American Chestnut Tree on Arbor Day

BALTIMORE, MD. Scientists have built a custom chromosome -- a package of genetic material assembled entirely from synthetic DNA.

This engineered chromosome belongs to yeast, but experts say it can help them understand how genes work in humans as well. And it could help make these tiny living factories better at producing everything from medicines to biofuels. Students were key to the project In a lab at Johns Hopkins University, students stitched together machine-made strands of DNA, the chemical that carries the genetic blueprints of life. Their goal: to assemble all 6,000 genes in the genome of yeast. Johns Hopkins geneticist Jef Boeke leads the class. He said yeast does familiar jobs, like turning grapes into wine, but they also do more than that. We have yeast that are used not just to make alcohol and bread, but also all kinds of chemicals, medicines, vaccines and fuels. And I think were going to see more and more of this in the future, said Boeke. And with genetic engineering, Boeke said, scientists could help yeast do those jobs better. Plus, these one-celled creatures share about a third of their genes with us. Studying their genes can teach us a lot about ourselves. Like us, yeast cells keep their genetic material in bundles of DNA known as chromosomes. Think of each chromosome as a book of genetic instructions, Boeke said. The book would be made up of chapters, the chapters would be made up of paragraphs and words and, ultimately letters, explained Boeke. And each gene is a word made up of letters of DNA, the chemical chain that forms the iconic twisted ladder shape. Boekes class has strung together all the words in one genetic book so far -- one chromosome out of yeasts 16. They engineered the new chromosome to let researchers shuffle genes around like a deck of cards. Some will have winning decks at making biofuels and some at making some other useful product, he said. Researchers say they are careful to consider the ethical implications of re-writing the code of life, but Boeke adds that his students are learning the basic tools of modern biology and getting excited about the possibilities. We could teach them how to do something at once very practical but at the same time amazing and unique, said Boeke. Macintosh Cornwell,a student at Johns Hopkins, said its helped him prepare for a career in science. The range of skills you learn and the amount of experience you get in such a small time period, its invaluable, really, said Cornwell. He and his class are on the cutting edge of this new world of biology.

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Scientists Build a Custom Chromosome

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Contrary to common scientific belief, many genes are switched "on" by default. These findings are from a study by Prof. Dr. Frank Holstege of University Medical Center (UMC) Utrecht that has been published in the April 24 edition of Cell.

Genetic differences between individuals affect the origin and treatment of diseases, a fact that has prompted more and more wide-scale genetic research. However, it seems that we sometimes lack very basic genetic knowledge.

Holstege's research shows that contrary to common opinion, many genes are by default actually switched "on". Given that DNA is wrapped in proteins, most scientists assumed that it could not be read by the cell. Transcription can only begin when so-called transcription factors bind to the DNA. Holstege and his colleagues show that nearly half of the transcription factors actually prevent the DNA from being read. It would seem that in most circumstances these genes should first be actively switched "off".

1,600 genes analyzed

Holstege and his colleagues used yeast as the model organism for their research. Yeast may seem far removed from humans, but its genes are controlled in exactly the same way as in human cells. Holstege et al. analyzed the role played by 1,600 genes, a quarter of all known yeast genes. They studied the effect that mutations in all those genes have on the gene expression of all other genes. This is the largest systematic study of the effect of mutation on gene expression to date.

Holstege has previously demonstrated that it is actually not necessarily useful to look at the effect of changes in just one gene. All genes are active in networks that are often organized in such a way that they can replace defective genes (Cell, December 10, 2010). The new study is the first step to mapping out the entire genetic control network.

"Comparative genetic research into patients and healthy subjects is very important," says Holstege. "It provides information on the cellular pathways associated with diseases. Our research shows, however, that it's hard to understand cells if you don't take the simultaneous activity of all genes into account."

Explore further: Research brings significant improvement in genetic analysis of tumours

Every tumour is unique and requires specific treatment. A thorough and complete analysis of the genetic activity in the tumour cells is necessary to determine the appropriate treatment. Researchers at TU ...

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Many genes are switched on by default

Deciphering Nature #39;s Alphabet - 3. Developing Genetic Tools
This film describes the conversion of these new DNA handling technologies into a viable business model that puts biology on the same plane as physics -- at least in terms of products it can...

By: GenomeTV

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Deciphering Nature's Alphabet - 3. Developing Genetic Tools - Video

3 hours ago Side view of a pregnant tsetse fly. Credit: Geoffrey M. Attardo

Mining the genome of the disease-transmitting tsetse fly, researchers have revealed the genetic adaptions that allow it to have such unique biology and transmit disease to both humans and animals.

The tsetse fly spreads the parasitic diseases human African trypanosomiasis, known as sleeping sickness, and Nagana that infect humans and animals respectively.

Throughout sub-Saharan Africa, 70 million people are currently at risk of deadly infection. Human African trypanosomiasis is on the World Health Organization's (WHO) list of neglected tropical diseases and since 2013 has become a target for eradication. Understanding the tsetse fly and interfering with its ability to transmit the disease is an essential arm of the campaign.

This disease-spreading fly has developed unique and unusual biological methods to source and infect its prey. Its advanced sensory system allows different tsetse fly species to track down potential hosts either through smell or by sight. This study lays out a list of parts responsible for the key processes and opens new doors to design prevention strategies to reduce the number of deaths and illness associated with human African trypanosomiasis and other diseases spread by the tsetse fly.

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"Tsetse flies carry a potentially deadly disease and impose an enormous economic burden on countries that can least afford it by forcing farmers to rear less productive but more trypanosome-resistant cattle." says Dr Matthew Berriman, co-senior author from the Wellcome Trust Sanger Institute. "Our study will accelerate research aimed at exploiting the unusual biology of the tsetse fly. The more we understand, the better able we are to identify weaknesses, and use them to control the tsetse fly in regions where human African trypanosomiasis is endemic."

The team, composed of 146 scientists from 78 research institutes across 18 countries, analysed the genome of the tsetse fly and its 12,000 genes that control protein activity. The project, which has taken 10 years to complete, will provide the tsetse research community with a free-to-access resource that will accelerate the development of improved tsetse-control strategies in this neglected area of research.

The tsetse fly is related to the fruit fly a favoured subject of biologists for more than 100 years but its genome is twice as large. Within the genome are genes responsible for its unusual biology. The reproductive biology of the tsetse fly is particularly unconventional: unlike most insects that lay eggs, it gives birth to live young that have developed to a large size by feeding on specialised glands in the mother.

Researchers found a set of visual and odour proteins that seem to drive the fly's key behavioural responses such as searching for hosts or for mates. They also uncovered the photoreceptor gene rh5, the missing link that explains the tsetse fly's attraction to blue/black colours. This behaviour has already been widely exploited for the development of traps to reduce the spread of disease.

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Genetic code of the deadly tsetse fly unraveled

PUBLIC RELEASE DATE:

24-Apr-2014

Contact: Tamlyn Oliver toliver@clinicalomics.com 914-740-2199 Mary Ann Liebert, Inc./Genetic Engineering News

New Rochelle, NY, April 24, 2014GEN Publishing recently introduced Clinical OMICs a semi-monthly digital publication focusing on the application of OMICs technologies in clinical settings. These advanced techniques, such as next-gen sequencing, are beginning to transform medical care just as they revolutionized basic life science research over the past decade-and-a-half.

"GEN's editors and reporters have written about the research use of pharmacogenomics, genomics, metabolomics, transcriptomics, etc. etc. for years," said John Sterling, editor-in-chief of Genetic Engineering & Biotechnology News (GEN). "The rapid advance of OMICs technologies has reached the point where we are convinced that the time is now for a new publication that shows how these diagnostic methodologies are dramatically impacting clinical practice."

Clinical OMICs is directed at clinical lab directors and managers, oncologists, infectious disease specialists, and cardiologists. Intended to serve as a resource for the development and standardization of best OMICs practices, Clinical OMICs provides critical information and insights on the trend toward personalized medicine.

The premier issue contains articles on translating OMICs into cancer biology and medicine, how payers are grappling with reimbursement issues, a profile of Lawrence Brody, who is overseeing NHGRI's new division of genomics and society, the move of next-gen sequencing systems into the clinic, and a case study of a genomics test for coronary artery disease. Late-breaking clinical OMICs news, OMICs-related clinical APPS, and new products are also featured.

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About Clinical OMICs

Clinical OMICs is brought to you by GEN Publishing, the parent company of Genetic Engineering & Biotechnology News.

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GEN Publishing introduces 'Clinical OMICs' digital publication

A CT scan showing a cochlear implant in the left ear of a guinea pig. Image: UNSW Australia Biological Resources Imaging Laboratory, NationalImaging Facility of Australia, and UNSW TranslationalNeuroscience Facility

Scientists have devised a strategy they hope will one day make bionic ears even sharper. The idea is to make neurons inside the ear sprout new branches and become more sensitive to signals from a cochlear implant.

The cochlear implant is arguably the most successful bionic device ever invented. More than 200,000 people with severe hearing loss have received one, allowing them to understand speech and hear things like barking dogs and fire alarms. But theres plenty of room for improvement.

Pitch perception is not so good, and that impacts music appreciation and hearing in a complex environment like a noisy room, said Gary Housley, a physiologist and neuroscientist at the University of New South Wales in Australia, and the senior author of a new study out today in Science Translational Medicine.

To appreciate what Housleys team did, you have to picture whats going on inside the inner ear. The bony, spiral cochlea is where sound waves get translated into the electrical language of neurons. Its essentially a coiled tube. The implant is thin like a wire, and it has an array of electrodes along its length. Surgeons thread it into the tube of the cochlea.A microphone worn on the ear converts sound into electrical signals and transmits them to the implant, thereby stimulating the auditory nerve directly and bypassing whatever part of the persons own hearing apparatus has broken down.

A cross section of the spiral tube of the cochlea shows the auditory nerve reaching up through the center. Image: Grays Anatomy, via WikiCommons

But a lot of information gets lost in the communication between the implant and the nerve.

Housley thinks one important reason is that in people with severe hearing loss, auditory nerve fibers degenerate and shrink into the bony core of the cochlea, farther away from the implant.

To try to overcome this communication breakdown, Housleys team borrowed some tricks from genetic engineering. We refer to it as closing the neural gap, he said.

Work by other scientists had suggested that growth factorschemicals that encourage neurons to grow new branchescouldimprove the performance of implants in lab animals. These studies used viruses to deliver genes encoding the growth factors, but Housleys team tried another strategy they think could be more precise.

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Genetic Tricks Could Make Bionic Ears Hear Better

4 hours ago 2014, Mary Ann Liebert, Inc., publishers

D-ribose is a commercially important sugar used as a sweetener, a nutritional supplement, and as a starting compound for synthesizing riboflavin and several antiviral drugs. Genetic engineering of Escherichia coli to increase the bacteria's ability to produce D-ribose is a critical step toward achieving more efficient industrial-scale production of this valuable chemical, as described in an article in Industrial Biotechnology.

In "Engineering Escherichia coli for D-Ribose Production from Glucose-Xylose Mixtures." Pratish Gawand and Radhakrishnan Mahadevan, University of Toronto, Canada, describe the metabolic engineering strategy they used to increase the yield of D-ribose from the genetically modified E. coli, which were able to produce D-ribose from mixtures of glucose and xylose. The authors propose future research directions for additional metabolic engineering and bioprocess optimization.

"The research article by Gawand and Mahadevan represents one of many ways that molecular biology is being deployed to expand Industrial Biotechnology development," says Co-Editor-in-Chief Larry Walker, PhD, Professor, Biological & Environmental Engineering, Cornell University, Ithaca, NY.

Explore further: Metabolically engineered E. coli producing phenol

More information: The article is available on the Industrial Biotechnology website.

Many chemicals we use in everyday life are derived from fossil resources. Due to the increasing concerns on the use of fossil resources, there has been much interest in producing chemicals from renewable resources through ...

The production of rare sugars has been very costly until now. A recent doctoral study indicates that their production can be made significantly more efficient with the help of genetically modified bacteria. ...

Food spoiling and poisoning caused by microbial contamination can cause major health, social, and economic problems. The broad scope of antimicrobial approaches to kill or prevent the growth of microorganisms ...

Combining systems metabolic engineering and downstream process, bio-based production of 5-aminovaleric acid and glutaric acid, important C5 platform chemicals, engineered in Escherichia coli could be demonstrated for the ...

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Engineered E. coli produces high levels of D-ribose