Category Archives: Genome

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

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"

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

How The Cancer Genome Atlas project is opening doors for curing cancer.
This is my Personal project and my goal is to raise awareness on this issue by making a short documentary on how The Cancer Genome Atlas Project forms a rese...

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How The Cancer Genome Atlas project is opening doors for curing cancer. - Video

Mar 05, 2015 by Winnie Lim

Research on the expression of viral DNA within the human genome furthers our understanding of human evolution and embryonic development

Singapore The human genome is the blueprint for human life, but much of this blueprint still remains a mystery. Researchers from A*STAR's Genome Institute of Singapore (GIS) have now discovered that sequences from old viruses that were thought to be useless, might contribute to the earliest cell types in the human life cycle. These newly discovered viral elements can be used to identify new types of embryonic stem cells, opening more possibilities to understanding human development and diseases.

The viral sequences that are the focus of the discovery are similar to retroviruses , but since they are a part of the human genome, they are known as endogenous retroviruses (ERV). ERVs are able to reinsert another copy of their own DNA into the human genome once they are activated. Since they mainly multiply their own DNA, they are sometimes referred to as 'selfish DNA'. Because of their 'selfishness', ERVs are potentially dangerous when they destroy genes that are essential to human life. In a study recently published in Cell Stem Cell, scientists describe that many ERVs are activated in cells from early embryos, but instead of being harmful, they might have become useful over the course of evolution.

Genes that are activated are transcribed into RNA to function. Therefore, scientists investigate the RNAs in the cell to identify active genes. "When we investigated public data from embryonic cells, we found that many RNAs originated from regions in the human genome that are ERVs," explained GIS Fellow Dr Jonathan Gke, who led the study. "We did not only observe isolated events, but systematic activation of these ERVs. Every cell type showed transcription of specific classes, something that is very unlikely to occur by chance".

"Many ERV elements are only fragments of the full viruses," added Dr Gke. "They maintain the activation sequence, but the RNA that they generate can be very different from the RNA that retroviruses generate". In many cases, these ERV-RNAs are even parts of RNAs generated from other genes. This way, ERVs might have evolved to gain a new function; they might have become a part of the blueprint for human life.

ERVs have been shown to play a role in diseases such as cancer. Because many ERVs are not expressed in the most widely used cell models, and they do not exist in mouse, scientists do not yet fully understand their function. The researchers now showed that a part of the ERVs which functions as activator can be used to identify cells that show expression of these ERV families. Such cells might overcome the limitations of current cell models to study the role and function of ERVs in development and disease.

"These are fascinating findings as the embryonic cells that express these ERV-derived RNAs are fundamental to the human life cycle. Now the big question is what they are actually doing." said Dr Guillaume Bourque, associate professor at the McGill University in Canada, who has worked on ERVs himself for many years. "From research with human embryonic stem cells, we know that ERVs have become essential, so it is quite likely that the ERVs described in this study contribute in a number of ways to human development."

"This is a very exciting study," said Prof Huck-Hui Ng, executive director of the GIS. "The results open up many new opportunities to better understand why and how embryonic cells are different from adult cells, and what role these newly discovered ERV-genes play. Some ERVs may even be involved in the formation of diseases, such as cancer."

Dr Gke's team at the GIS plans to take their research further. "We are now developing new algorithms that will help us identify additional ERVs in the human genome, and we try to isolate cells that express these ERV-RNAs. This way we will be able to study their function and how they contribute to human diseases".

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Scientists discover new roles for viral genes in the human genome

Triple Helix pre-release video: Genome Eta
Snow canceled school on robot bag day, so the multimedia team won #39;t have the opportunity to make their release video for a few days. I #39;m sure it will be nice...

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Triple Helix pre-release video: Genome Eta - Video

"Thank You" HudsonAlpha Genome Circle 2015
HudsonAlpha appreciates the support of Genome Circle members. For more information about the HudsonAlpha Genome Circle, go to http://hudsonalpha.org/support-...

By: HudsonAlpha Institute for Biotechnology

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"Thank You" HudsonAlpha Genome Circle 2015 - Video

Human Genome, Movie Music, without vox, Virgo Rouge
Original composition and all instrumentation: Marissa Elienne aka Virgo Rouge .Copyright 2015. All rights reserved. There will be a vocal line added to this ...

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Human Genome, Movie Music, without vox, Virgo Rouge - Video

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Newswise (MEMPHIS, Tenn. March 6, 2015) The St. Jude Childrens Research HospitalWashington University Pediatric Cancer Genome Project reports that a highly aggressive form of leukemia in infants has surprisingly few mutations beyond the chromosomal rearrangement that affects the MLL gene. The findings suggest that targeting the alteration is likely the key to improved survival. The research appeared online ahead of print this week in the scientific journal Nature Genetics.

The study is the most comprehensive analysis yet of this rare but aggressive subtype of pediatric acute lymphoblastic leukemia (ALL) that occurs during the first year of life and is sometimes diagnosed at birth. The leukemia cells of up to 80 percent of infants with ALL have a chromosomal rearrangement that fuses the MLL gene to a gene on a different chromosome. The resulting MLL fusion gene encodes an abnormal protein. The fusion protein plays a key role in transforming normal blood cells into leukemia cells.

Researchers used whole genome sequencing and other techniques to identify the genetic alterations in 65 infants with ALL, including 47 with the MLL rearrangement. Scientists were surprised to find that despite being an aggressive leukemia, the MLL rearranged subtype had among the lowest mutation rates reported for any cancer.

These results show that to improve survival for patients with this aggressive leukemia we need to develop drugs that target the abnormal proteins produced by the MLL fusion gene or that interact with the abnormal MLL fusion protein to shut down the cellular machinery that drives their tumors, said senior and co-corresponding author James R. Downing, M.D., St. Jude president and chief executive officer. That will not be easy, but this study found no obvious cooperating mutations to target.

St. Jude researchers are working to identify compounds and develop combination therapies to improve cure rates for infants with the MLL rearrangement. Nationally, 85 percent of pediatric ALL patients now enjoy long-term, cancer free survival compared to 28 to 36 percent of infants with the high-risk subtype.

We frequently associate a cancers aggressiveness with its mutation rate, but this work indicates that the two dont always go hand-in-hand, said co-author Richard K. Wilson, Ph.D., director of The Genome Institute at Washington University School of Medicine in St. Louis. Still, our findings provide a new direction for developing more effective treatments for these very young patients.

The other corresponding authors are Tanja Gruber, M.D., Ph.D., assistant member in the St. Jude Department of Oncology, and Anna Andersson, Ph.D., formerly of St. Jude and now of Lund University, Sweden. Andersson and Jing Ma, Ph.D., of the St. Jude Department of Pathology, are co-first authors.

Almost half of infants with MLL rearranged ALL had activating mutations in a biochemical pathway called the tyrosine kinase-phosphoinositide-3-kinase (PI3K)-RAS pathway. Surprisingly, the mutations were often present in only some of the leukemic cells. Researchers analyzed leukemia cells in infants whose cancer returned after treatment and found that at the time of relapse the cells lacked the pathway mutations. The fact that the mutations were often lost at relapse suggests that patients are unlikely to benefit from therapeutically targeting these mutations at diagnosis, Downing said.

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Chromosomal Rearrangement Is the Key to Progress Against Aggressive Infant Leukemia

Investigating the Human Genome Insights into Human Variation and Disease Susceptibility
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Investigating the Human Genome Insights into Human Variation and Disease Susceptibility - Video

Melbourne Conversations - Personalised Medicine: Me and My Genome
Global genomics expert Professor Michael Snyder from Stanford University sequenced his genome and got a shock! Hear his story, get the latest on the work aro...

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Melbourne Conversations - Personalised Medicine: Me and My Genome - Video