Showing posts with label Genetic. Show all posts
Showing posts with label Genetic. Show all posts

Fly eyes help researchers 'see' new proteins involved in memory

[ScienceNology] - With more than 1,500 eyes, not much escapes the fruit fly's sight. Now, a new research report in the journal GENETICS (http://www.genetics.org), describes how researchers from the United States and Ireland used those eyes to "see" new proteins necessary for memory. In addition to shedding light on this critical neurological process, the study also provides information on a form of mental retardation in humans.

"Understanding translational control mechanisms in the brain teaches us how the brain learns and adapts, and will inform the design of treatments for specific types of neurologic disease," said Dr. Anne-Marie Cziko, at the University of Arizona and co-author of the study.

Specifically, the scientists found that the "fragile X mental retardation protein," which plays a crucial role in the cellular processes involved in learning and memory, needs five other proteins to function normally. The scientists identified these proteins using an artificial system of increasing fragile X mental retardation protein in the eyes of fruit flies. Its high level leads to visible deformities in a fly's eyes. To test the requirement of various candidate proteins for function of the fragile X mental retardation protein, the researchers genetically modified the flies to prevent them from making each candidate protein. They found that loss of any one of the five proteins caused the fruit fly's eye to be significantly less deformed, revealing that each is required for function of the fragile X mental retardation protein.

Because previous work suggested that the fragile X protein regulates gene expression via an important group of small RNAs called "microRNAs," the scientists tested whether the proteins they identified were required for a specific microRNA named "bantam" to function in fruit flies. The researchers performed these experiments by removing copies of the identified proteins from the fly. Instead of looking at the flies' eyes, the researchers looked inside the flies using a fluorescent protein that indicates how well bantam is functioning. The investigators were surprised to find that none of the five proteins identified in the study had an effect on bantam. Even more surprisingly, neither did the fragile X mental retardation protein.

This finding and the identification of the five new proteins that interact with the fragile X mental retardation protein give new insight into additional and alternative functions of fragile X mental retardation protein. They also indicate the need for more study into the fragile X mental retardation protein's function itself.

"Any college student on the eve of final exams will tell you that truly understanding—and possibly manipulating—how our brains store information is the 'Holy Grail' of neurological research," said Mark Johnston, Editor-in-Chief of the journal GENETICS. "Although college students are advised to continue hitting the books, this area of research holds tremendous promise for millions or people with neurological diseases and disabilities, as well as for those with learning disorders."


Details: Anne-Marie J. Cziko, Cathal T. McCann, Iris C. Howlett, Scott A. Barbee, Rebecca P. Duncan, Rene Luedemann, Daniela Zarnescu, Konrad E. Zinsmaier, Roy R. Parker, and Mani Ramaswami
Genetic Modifiers of dFMR1 Encode RNA Granule Components in Drosophila
GENETICS 2009 182: 1051�: http://www.genetics.org/cgi/content/abstract/182/4/1051



A Research report from Genetics.org , via EurekAlert! , 24 August 2009

Photo credit to http://static.guim.co.uk

CSHL scientists develop new method to detect copy number variants using DNA sequencing technologies

[ScienceNology] - A research team led by Associate Professor Jonathan Sebat, Ph.D., of Cold Spring Harbor Laboratory (CSHL) has developed a sensitive and accurate way of identifying gene copy number variations (CNVs). The method, which is described in a paper published online ahead of print in Genome Research, uses new DNA sequencing technologies to look for regions of the genome that vary in copy number between individuals in the population. Capable of detecting a wide range of different classes of CNVs, large and small, this method allows researchers to extract more genetic information from the complete genome sequence of an individual.

CNVs are regions of the genome that vary in the number of copies between individuals. These variants were once considered to be anomalies that occurred rarely among healthy individuals. As the result of a discovery by CSHL Professor Michael Wigler and Dr. Sebat in 2004, CNVs are now recognized as a major source of human genetic variation and methods for detecting CNVs have proven to be an effective approach for identifying genetic risk factors for disease.

Genome sequencing technologies are improving at a rapid pace. The current challenge is to find ways to extract all of the genetic information from the data. One of the biggest challenges has been the detection of CNVs. Sebat, in collaboration with Seungtai Yoon of CSHL and Kenny Ye, Ph.D., at the Albert Einstein College of Medicine, developed a statistical method to estimate DNA copy number of a genomic region based on the number of sequences that map to that location (or "read depth"). When the genomes of multiple individuals are compared, regions that differ in copy number between individuals can be identified.

The new method allows the detection of small structural variants that could not be detected using earlier microarray-based methods. This is significant because most of the CNVs the genome are less than 5000 nucleotides in length. The new method is also able to detect certain classes of CNVs that other sequencing-based approaches struggle with, particularly those located in complex genomic regions where rearrangements occur frequently.

The development of this novel method is timely. The 1000 Genomes Project was launched in 2008, as an international effort to sequence the genomes of 2000 individuals across geographic and ethnic regions to catalog human genetic variation. Sebat's team along with many other groups has contributed to the production and analysis of these data.

This innovation improves the detection of structural variants from whole genome sequence data, which will lead to improved sensitivity to detect disease-causing CNVs.


"Sensitive and accurate detection of copy number variants using read depth of coverage" can be found online at http://genome.cshlp.org/content/early/2009/08/05/gr.092981.109.long. The full citation is: Seungtai Yoon, Zhenyu Xuan, Vladimir Makarov, Kenny Ye and Jonathan Sebat. Support for this work was provided by the National Human Genome Research Institute, part of the National Institutes of Health.


A Research from Cold Spring Harbour Laboratory, via EurekAlert! , 24 August 2009