Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Microarrays as phenotype

11.04.2005


Microarrays provide a method of quantifying the expression and order of genes in a particular genome -- acting as a surrogate measure of cell physiology, said researchers at Baylor College of Medicine in a report that appears online today in the journal Nature Genetics.



"Microarray data are good phenotypes to determine the order of genes and are a good surrogate measure of cell status," said Dr. Gad Shaulsky, associate professor of molecular and human genetics at BCM.

Microarrays are fairly new technology that can help scientists understand how genes interact as well as how they are regulated by networks within the cell. They are created by the placement of tiny droplets of functional DNA on glass slides. Then researchers attach fluorescent labels to nucleic acids (DNA or RNA) from the cells under study. These labeled nucleic acids are allowed to bind to the DNA on the slides. Researchers then use a microscope to measure how much of a specific nucleic acid is present.


Genotype is the genetic fingerprint of a particular cell. Phenotype is the outward manifestation of the genotype. For example, a person may have genes for eye color. That is that individual’s genotype. Blue eyes is the phenotype.

The microarray data Shaulsky and his collaborators used show that they can determine the order in which genes act in a cascade that results in a particular phenotype.

Shaulsky and his co-authors performed their work in Dictyostelium (Dictyostelium discoideum), a form of soil amoeba used in the laboratory because many of its 10,000 genes are homologues or equivalents of genes found in humans.

Using microarray data alone, they determined the orders in which genes function in a particular pathway in that organism. The protein kinase A (PKA) signaling pathway occurs when the organism encounters starvation. The pathway enables the single cells to combine into a multi-cell organism.

"We pretended we did not know the order of genes in the pathway," said Shaulsky. "We were able to reconstruct the pathway from the microarray data. This means the microarray provides a good phenotype that is quantitative. We can prove that gene A comes before gene B and give mathematical support for these findings."

"This is a proof of principle that we set out to do – assessing the function of unknown genes is feasible," said Shaulsky. "It can be done with a microarray phenotype."

Others who participated in the research included Drs. Nancy Van Driessche, Ezgi O. Booth, Paul Hill and Adam Kuspa, all of Baylor College of Medicine; and Janez Demsar, Peter Juvan and Blaz Zupan of the Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.

Ross Tomlin | EurekAlert!
Further information:
http://www.bcm.tmc.edu

More articles from Life Sciences:

nachricht Climate Impact Research in Hannover: Small Plants against Large Waves
17.08.2018 | Leibniz Universität Hannover

nachricht First transcription atlas of all wheat genes expands prospects for research and cultivation
17.08.2018 | Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Color effects from transparent 3D-printed nanostructures

New design tool automatically creates nanostructure 3D-print templates for user-given colors
Scientists present work at prestigious SIGGRAPH conference

Most of the objects we see are colored by pigments, but using pigments has disadvantages: such colors can fade, industrial pigments are often toxic, and...

Im Focus: Unraveling the nature of 'whistlers' from space in the lab

A new study sheds light on how ultralow frequency radio waves and plasmas interact

Scientists at the University of California, Los Angeles present new research on a curious cosmic phenomenon known as "whistlers" -- very low frequency packets...

Im Focus: New interactive machine learning tool makes car designs more aerodynamic

Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.

When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...

Im Focus: Robots as 'pump attendants': TU Graz develops robot-controlled rapid charging system for e-vehicles

Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.

Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....

Im Focus: The “TRiC” to folding actin

Proteins must be folded correctly to fulfill their molecular functions in cells. Molecular assistants called chaperones help proteins exploit their inbuilt folding potential and reach the correct three-dimensional structure. Researchers at the Max Planck Institute of Biochemistry (MPIB) have demonstrated that actin, the most abundant protein in higher developed cells, does not have the inbuilt potential to fold and instead requires special assistance to fold into its active state. The chaperone TRiC uses a previously undescribed mechanism to perform actin folding. The study was recently published in the journal Cell.

Actin is the most abundant protein in highly developed cells and has diverse functions in processes like cell stabilization, cell division and muscle...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

LaserForum 2018 deals with 3D production of components

17.08.2018 | Event News

Within reach of the Universe

08.08.2018 | Event News

A journey through the history of microscopy – new exhibition opens at the MDC

27.07.2018 | Event News

 
Latest News

Smallest transistor worldwide switches current with a single atom in solid electrolyte

17.08.2018 | Physics and Astronomy

Robots as Tools and Partners in Rehabilitation

17.08.2018 | Information Technology

Climate Impact Research in Hannover: Small Plants against Large Waves

17.08.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>