Monthly Archives: March 2015

gUIDEbook gRNA Design - for CRISPR genome editing experiments
Successful CRISPR genome editing relies on the quality of the gRNA design, and that requires the best bioinformatic software. gUIDEbook from Desktop Genetic...

By: Horizon Discovery

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gUIDEbook gRNA Design - for CRISPR genome editing experiments - Video

A genome study of the famed Darwin finch species on the Galapagos and Cocos islands has unveiled a gene behind the 15 species' remarkable variation of beaks, a feature that helped inspire the father of evolutionary theory.

The study of 120 individual birds from across the South American island chain finds that a single species radiated into more than a dozen others over the past million years, a change fueled by hybridization.

The wide variety of beak shape and size among finches on the archipelago has become an iconic foundational story behind Charles Darwin's "On the Origin of Species," published in 1859 -- even though he misidentified them at first and gave them scant mention in the treatise. But they have come to represent a textbook example of how species develop through random variation and the forces of natural selection.

"He wrote that it looked like this was one species that changed into multiple species, and particularly through the change of the beak shape to utilize food," said Uppsala University geneticist Leif Andersson, co-author of the study published online Wednesday in the journal Nature. "Our data fit perfectly with that.

British biologist Peter and Rosemary Grant, of Princeton University, have spent 40 years studying the subtle changes in the birds, and published a startling example of natural selection unfolding among a pair of species on one of the islands. The two areco-authors of the current report, which used some of the DNA samples they collected.

"You can imagine how satisfying it is for us after all those years in the field to be able to discover a gene that underpins our findings of evolution by natural selection," Peter Grant said.

The gene, called ALX1, is located on a swath of the genome whose coding has been remarkably consistent for ages, until changes altered the production of four proteins, and that gene variation came to dominate.

"As many changes that have occurred over 300 million years have occurred during the last million years on the Galapagos, said Andersson.

The finches are descended from a sharp-billed South American tanager that arrived on the islands about 1.5 million years ago, according to the study. Warbler finches split earliest, about 900,000 years ago, with ground and tree finches constituting the most recent radiation, about 100,000 to 300,000 years ago, according to the study.

But during that time, there was much interbreeding that allowed genes to flow across species, leaving them with a wide variety of beak sizes and shapes, the study suggests.

Read more:
Genome study unmasks evolution of Darwin's finches

BUFFALO, N.Y., Feb. 24 (UPI) -- Bladderworts are a genus of carnivorous plants that prefer freshwater environs or very wet soils. And as a new study finds, at least one bladderwort variety -- in terms of genomics, anyways -- does more with less.

Researchers at the University of Buffalo recently sequenced the genome of Utricularia gibba, one of the most common types of bladderworts called humped or floating bladderwort. Despite its many unique biological features, the quirky aquatic plant has a remarkably short genome.

Inside that short genome are the genetic sequences that enable its odd characteristics. Floating bladderwort forgoes roots, traps prey with vacuum pressure, sprouts small thread-like branches, puts off beautiful yellow flowers and does it all while thriving in aquatic environment.

As the bladderwort's odd lifestyle suggests -- and as the new analysis proved -- a short genome doesn't necessarily translate to a dearth of genetic material. Researchers found that despite its shrunken genome, floating bladderwort boasts more genes than a number of more common plants, including the grape, coffee or papaya plants.

The research suggests that humped bladderwort is more than just economical, it's the opposite of repetitive. It's idiosyncratic -- and especially fluctuant. And it is this variability that allowed the bladderwort to pack so much genetic code into such a small space.

"The story is that we can see that throughout its history, the bladderwort has habitually gained and shed oodles of DNA," study leader Victor Albert, a biologist at Buffalo, explained in a press release. "With a shrunken genome, we might expect to see what I would call a minimal DNA complement: a plant that has relatively few genes -- only the ones needed to make a simple plant. But that's not what we see."

But constantly deleting genes to make up for its genetic replications and adaptations, the floating bladderwort seems have become exceptionally good a ridding itself of junk DNA, sequences that have little to no genetic or biological value.

"When you have the kind of rampant DNA deletion that we see in the bladderwort, genes that are less important or redundant are easily lost," Albert said. "The genes that remain -- and their functions -- are the ones that were able to withstand this deletion pressure, so the selective advantage of having these genes must be pretty high."

"Accordingly, we found a number of genetic enhancements, like the meat-dissolving enzymes, that make Utricularia distinct from other species," Albert added.

While floating bladderwort contains only a small percentage of junk DNA, almost 90 percent of the human genome is made up of throwaway genes.

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Aquatic plant has tiny genome but lots and lots of genes

Hints for how to improve the treatment of parasitic infection might lie within the parasite's own genetic code

IMAGE:Tiny parasitic hookworms infect nearly half a billion people worldwide -- almost exclusively in developing countries -- causing health problems ranging from gastrointestinal issues to cognitive impairment and stunted growth... view more

Credit: Yan Hu/Aroian Lab/UC San Diego

Tiny parasitic hookworms infect nearly half a billion people worldwide--almost exclusively in developing countries--causing health problems ranging from gastrointestinal issues to cognitive impairment and stunted growth in children. By sequencing and analyzing the genome of one particular hookworm species, Caltech researchers have uncovered new information that could aid the fight against these parasites.

The results of their work were published online in the March 2 issue of the journal Nature Genetics.

"Hookworms infect a huge percentage of the human population. Getting clean water and sanitation to the most affected regions would help to ameliorate hookworms and a number of other parasites, but since these are big, complicated challenges that are difficult to address, we need to also be working on drugs to treat them," says study lead Paul Sternberg, the Thomas Hunt Morgan Professor of Biology at Caltech and a Howard Hughes Medical Institute investigator.

Medicines have been developed to treat hookworm infections, but the parasites have begun to develop resistance to these drugs. As part of the search for effective new drugs, Sternberg and his colleagues investigated the genome of a hookworm species known as Ancylostoma ceylanicum. Other hookworm species cause more disease among humans, but A. ceylanicum piqued the interest of the researchers because it also infects some species of rodents that are commonly used for research. This means that the researchers can easily study the parasite's entire infection process inside the laboratory.

The team began by sequencing all 313 million nucleotides of the A. ceylanicum genome using the next-generation sequencing capabilities of the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. In next-generation sequencing, a large amount of DNA--such as a genome--is first reproduced as many very short sequences. Then, computer programs to match up common sequences in the short strands to piece them into much longer strands.

"Assembling the short sequences correctly can be a relatively difficult analysis to carry out, but we have experience sequencing worm genomes in this way, so we are quite successful," says Igor Antoshechkin, director of the Jacobs Laboratory.

Their sequencing results revealed that although the A. ceylanicum genome is only about 10 percent of the size of the human genome, it actually encodes at least 30 percent more genes--about 30,000 in total, compared to approximately 20,000-23,000 in the human genome. However, of these 30,000 genes, the essential genes that are turned on specifically when the parasite is wreaking havoc on its host are the most relevant to the development of potential drugs to fight the worm.

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Fighting a worm with its own genome

IMAGE:This is a figure depicting four regulatory models for genome-edited crops. view more

Credit: Araki, M. and Ishii, T./Trends in Plant Science 2015

A survey of rice, wheat, barley, fruit, and vegetable crops found that most mutants created by advanced genetic engineering techniques may be out of the scope of current genetically modified organism (GMO) regulations. In a review of these findings, published in the February 25 issue of the Cell Press journal Trends in Plant Science, two bioethicists from Hokkaido University propose new regulatory models for genome-edited crops and declare a call to action for clarifying the social issues associated with such genetically engineered crops.

"Modern genome editing technology has allowed for far more efficient gene modification, potentially impacting future agriculture," says Tetsuya Ishii, PhD, of Hokkaido University's Office of Health and Safety. "However, genome editing raises a regulatory issue by creating indistinct boundaries in GMO regulations because the advanced genetic engineering can, without introducing new genetic material, make a gene modification which is similar to a naturally occurring mutation."

Under current regulations, a GMO is a living organism that has been altered by a novel combination of genetic material, including the introduction of a transgene. Advanced genetic engineering technologies, including ZFN, TALEN, and CRISPR/Cas9, raise regulatory issues because they don't require transgenes to make alterations to the genome. They can simply pluck out a short DNA sequence or add a mutation to an existing gene.

"Genome editing technology is advancing rapidly; therefore it is timely to review the regulatory system for plant breeding by genome editing," says Dr. Ishii. "Moreover, we need to clarify the differences between older genetic engineering techniques and modern genome editing, and shed light on various issues towards social acceptance of genome edited crops."

In their study, Dr. Ishii and a member of his research staff, Motoko Araki, present four regulatory models in order to resolve the indistinct regulatory boundaries that genome editing has created in GMO regulations. They propose that the most stringent regulation (in which most of the mutants are subject to the regulations, whereas only a portion of deletion and insertion mutants fall outside the regulations) should be initially adopted and gradually relaxed because the cultivation and food consumption of genome-edited crops is likely to increase in the near future.

While policy-level discussions about the regulations of genome-edited organisms are slowly taking place around the world, according to Dr. Ishii, his study will serve as a basis for the conversation with regulatory agencies in the world as well as the Japanese Ministry of the Environment.

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Trends in Plant Science, Araki, M. and Ishii, T.: "Towards social acceptance of plant breeding by genome-editing"

Originally posted here:
Regulating genome-edited crops that (according to current regulations) aren't GMOs