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The Jetlag of a Glowing Fish and More: Press Release from PLoS Biology
January 25, 2005What Does an Airline Traveler Have in Common with a Glowing Fish?
In William Gibson's novel Pattern Recognition, the protagonist posits a theory of jet lag: "Souls can't move that quickly, and are left behind, and must be awaited, upon arrival, like lost luggage." Science has yet to address the issue of a spiritual speed limit, but it is generally accepted that jet lag actually results from the upset of the body's circadian clock, a biochemical pacemaker that dictates daily rhythms in sleep and wakefulness as well as body temperature and metabolic activity.
Circadian rhythms are regulated by changes in daylight cycles, but how and when they first develop is not well understood. Reported this week in the open-access journal PLoS Biology, Maki Kaneko and Gregory Cahill have created a new tool for investigating the components of the circadian clock in vertebrates: a zebrafish that luminesces (glows) in sync with the periodicity of its circadian clock. They find, contrary to earlier studies, that aspects of circadian rhythms are not hardwired into the embryo, but develop in specific stages.
To do this, the researchers created a transgene that places expression of the firefly luciferase gene under the control of the promoter of the zebrafish circadian gene period3 (per3). Each cell of the transgenic fish has one normal copy of the per3 gene and one copy of the period3-luciferase fusion gene (per3-luc). Therefore, whenever per3 expression is normally turned on in a cell, the cell produces Per3 protein and also produces the luciferase protein.
Kaneko and Cahill anticipate that these transgenic zebrafish will be quite useful in examining the molecular machinery of the vertebrate circadian clock. For example, researchers can use the per3-luc transgenic zebrafish in forward genetic screens to identify new molecular regulators of circadian rhythms. What is more, luminescence can be measured quickly and noninvasively, making this animal an ideal candidate for high-throughput screening aimed at identifying components of the circadian clock in the zebrafish. Thanks to luminescent fish, scientists may someday gain enough insight to make jet lag a thing of the past.
Citation: Kaneko M, Cahill G (2005) Light-dependent development of circadian gene expression in transgenic zebrafish. PLoS Biol 3 (2): e34.
The published article will be accessible to your readers at:
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0030034
Press-only preview of the article: http://www.plos.org/downloads/plbi-03-02-cahill.pdf
CONTACT:
Gregory Cahill
University of Houston
4800 Calhoun Rd.
Houston, TX USA 77204-5001
+1-713-743-2694
+1-713-743-2636 (fax)
gcahill@uh.edu
******************************
Rice Genome Approaches Completion
A large group of scientists led by the Beijing Institute of Genomics has published in the freely-available online journal PLoS Biology a much improved, near-complete genome analysis of the indica and japonica subspecies of Oryza sativa, which are eaten in India and China, and Japan, respectively. The analysis team, led by Gane Ka-Shu Wong, provides important insights into the evolution of rice.
The key to the improvement in the genome sequence analysis is that the researchers have used the combined DNA sequence data from the two subspecies to facilitate the sequence assembly. The result is a nearly 1,000-fold increase in contiguity for the two genome sequences relative to the existing sequence data.
The researchers have used their improved genome sequence to investigate the evolutionary history of rice. Central to evolution is the development of new functions through mutation of existing genes. But when mutations occur in functional genes, the result is rarely beneficial, so it is thought that evolution is more likely to proceed first by duplicating existing genes and then experimenting on the "backup" copy of the gene.
Wong and colleagues report that there is evidence in the rice DNA sequences for a whole-genome duplication event just before the grasses diverged from other flowering plants, about 55-70 million years ago. This genome duplication may have played a role in the origin of the grasses, which then spread rapidly across the world to provide important sources of food that, among other things, possibly influenced human evolution.
Analysis of the rice genomes also indicates that there is massive ongoing duplication of individual genes. These individual gene duplications provide a continuous source of raw material for gene genesis and very likely contribute to the differences between members of the grass family. Now the challenge is to use the rice sequences as a basis for detailed genetic analyses of additional cereal crops and for the development of improved strains of not only rice, but wheat, maize, and other important food crops.
Citation: Yu J, Wang J, Wei L, Songgang L, Heng L, et al. (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3 (2): e38.
The published article will be accessible to your readers at:
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0030038
Press-only preview of the article: http://www.plos.org/downloads/plbi-03-02-wong.pdf
Related image for press use: http://www.plos.org/downloads/plbi-03-02-wong.jpg
Caption for image: Child dressed in traditional Han suit, wanting to share his fully cooked rice genome with the rest of the world, after reserving a small portion for himself. Photography by Lei Xu and Fang Chen, Beijing Institute of Genomics. Child model: Wensen Cai.
CONTACT:
Gane Ka-Shu Wong
University of Washington Genome Center
Beijing Institute of Genomics
Seattle, WA USA 98195
+86-135-215-754-44
gksw@genomics.org.cn
******************************
A Bug's Life: Aging and Death in E. coli
Can organisms such as bacteria age? The assumption has been that cells that divide symmetrically do not age and are functionally immortal. In a study published in the premier open-access journal PLoS Biology Eric Stewart and colleagues have now overturned this idea by analyzing repeated cycles of reproduction in Escherichia coli, a bacteria that reproduces without a juvenile phase and with an apparently symmetric division - revealing that these bacteria, like other organisms, have not escaped immortality.
E. coli reproduces by dividing in the middle. Each resultant cell inherits an old end or pole and a new pole, which contain slightly different components, so although they look the same, they are physiologically asymmetrical. At the next division, one cell inherits the old pole again (plus a brand new pole), while the other cell inherits a not-quite-so-old pole and a new pole. Thus, Stewart and co-workers reasoned, an age in divisions can be assigned to each pole and hence to each cell. The researchers used automated time-lapse microscopy to follow all the cell divisions in 94 colonies, each grown from a single fluorescently labeled E. coli cell. In all, the researchers built up a lineage for 35,049 cells in terms of which pole-old or new-each cell had inherited at each division during its history. They found that the cells inheriting old poles had a reduced growth rate, decreased rate of offspring formation, and increased risk of dying compared with the cells inheriting new poles. Thus, the "old pole" cell is effectively an aging parent repeatedly producing rejuvenated offspring.
Stewart and his colleagues conclude that no life strategy is immune to the effects of aging and suggest that this may be because immortality is too costly or is mechanistically impossible. This may be bad news for people who had hoped that advances in science might eventually lead to human immortality. Nevertheless, E. coli should now provide an excellent genetic platform for the study of the fundamental mechanisms of cellular aging and so could provide information that might ameliorate some of the unpleasantness of the human aging process.
Citation: Stewart E, Madden R, Paul G, Taddei F (2005) Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol 3 (2): e45.
The published article will be accessible to your readers at:
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0030045
Press-only preview of the article: http://www.plos.org/downloads/plbi-03-02-stewart.pdf
Related image for press use: http://www.plos.org/downloads/plbi-03-02-stewart.jpg
Caption for image: "What is true for E. coli is true for the elephant." Quote by Jacques Monod. This false color image shows a growing microcolony of E. coli, where the cells are colored by age (in numbers of divisions). The oldest cells are red, and the youngest blue. Photograph by Eric Stewart and Stefanie Timmermann, Inserm U571, Faculté de Médecine Necker Enfants-Malades, Paris, France.
CONTACT:
Eric Stewart
INSERM U571 Génétique Moléculaire Evolutive et Médicale
156 Rue de Vaugirard
Paris, France 75015
+33-(0)-1-40-61-53-27
+33-(0)-1-40-61-53-22 (fax)
stewart@necker.fr
Public Library Of Science
Citation: Yu J, Wang J, Wei L, Songgang L, Heng L, et al. (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3 (2): e38.
The published article will be accessible to your readers at:
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0030038
Press-only preview of the article: http://www.plos.org/downloads/plbi-03-02-wong.pdf
Related image for press use: http://www.plos.org/downloads/plbi-03-02-wong.jpg
Caption for image: Child dressed in traditional Han suit, wanting to share his fully cooked rice genome with the rest of the world, after reserving a small portion for himself. Photography by Lei Xu and Fang Chen, Beijing Institute of Genomics. Child model: Wensen Cai.
CONTACT:
Gane Ka-Shu Wong
University of Washington Genome Center
Beijing Institute of Genomics
Seattle, WA USA 98195
+86-135-215-754-44
gksw@genomics.org.cn
******************************
A Bug's Life: Aging and Death in E. coli
Can organisms such as bacteria age? The assumption has been that cells that divide symmetrically do not age and are functionally immortal. In a study published in the premier open-access journal PLoS Biology Eric Stewart and colleagues have now overturned this idea by analyzing repeated cycles of reproduction in Escherichia coli, a bacteria that reproduces without a juvenile phase and with an apparently symmetric division - revealing that these bacteria, like other organisms, have not escaped immortality.
E. coli reproduces by dividing in the middle. Each resultant cell inherits an old end or pole and a new pole, which contain slightly different components, so although they look the same, they are physiologically asymmetrical. At the next division, one cell inherits the old pole again (plus a brand new pole), while the other cell inherits a not-quite-so-old pole and a new pole. Thus, Stewart and co-workers reasoned, an age in divisions can be assigned to each pole and hence to each cell. The researchers used automated time-lapse microscopy to follow all the cell divisions in 94 colonies, each grown from a single fluorescently labeled E. coli cell. In all, the researchers built up a lineage for 35,049 cells in terms of which pole-old or new-each cell had inherited at each division during its history. They found that the cells inheriting old poles had a reduced growth rate, decreased rate of offspring formation, and increased risk of dying compared with the cells inheriting new poles. Thus, the "old pole" cell is effectively an aging parent repeatedly producing rejuvenated offspring.
Stewart and his colleagues conclude that no life strategy is immune to the effects of aging and suggest that this may be because immortality is too costly or is mechanistically impossible. This may be bad news for people who had hoped that advances in science might eventually lead to human immortality. Nevertheless, E. coli should now provide an excellent genetic platform for the study of the fundamental mechanisms of cellular aging and so could provide information that might ameliorate some of the unpleasantness of the human aging process.
Citation: Stewart E, Madden R, Paul G, Taddei F (2005) Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol 3 (2): e45.
The published article will be accessible to your readers at:
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0030045
Press-only preview of the article: http://www.plos.org/downloads/plbi-03-02-stewart.pdf
Related image for press use: http://www.plos.org/downloads/plbi-03-02-stewart.jpg
Caption for image: "What is true for E. coli is true for the elephant." Quote by Jacques Monod. This false color image shows a growing microcolony of E. coli, where the cells are colored by age (in numbers of divisions). The oldest cells are red, and the youngest blue. Photograph by Eric Stewart and Stefanie Timmermann, Inserm U571, Faculté de Médecine Necker Enfants-Malades, Paris, France.
CONTACT:
Eric Stewart
INSERM U571 Génétique Moléculaire Evolutive et Médicale
156 Rue de Vaugirard
Paris, France 75015
+33-(0)-1-40-61-53-27
+33-(0)-1-40-61-53-22 (fax)
stewart@necker.fr
Public Library Of Science
Genome Current Events and Genome News RSSTime of day matters to thirsty trees, U of T researcher discovers
The time of day matters to forest trees dealing with drought, according to a new paper produced by a research team led by Professor Malcolm Campbell, University of Toronto Scarborough's vice-principal for research and colleagues in the department of cell and systems biology at the St. George campus.
Genetic analysis helps dissect molecular basis of cardiovascular disease
Using highly precise measurements of plasma lipoprotein concentrations determined by nuclear magnetic resonance spectroscopy (NMR), researchers led by Daniel Chasman at Brigham and Women's Hospital and Harvard Medical School in Boston, MA, the Framingham Heart Study in Framingham, and the PROCARDIS consortium in Stockholm, Sweden and Oxford, England performed genetic association analysis across the whole genome among 17,296 women of European ancestry from the Women's Genome Health Study.
Gene mismatch influences success of bone marrow transplants
A commonly inherited gene deletion can increase the likelihood of immune complications following bone marrow transplantation, an international team of researchers reports in the November 22 advance online issue of Nature Genetics.
Scientists at UA, collaborating institutions decode maize genome
Scientists from the University of Arizona led by Arizona Genomics Institute director Rod A. Wing and from collaborating institutions have deciphered the complete genetic code of the maize plant for the first time.
Ancestry attracts, but love is blind
People preferentially marry those with similar ancestry, but their decisions are not necessarily based on hair, eye or skin colour.
WPI Researchers Take Aim at Hard-to-Treat Fungal Infections
A team of researchers at the Worcester Polytechnic Institute (WPI) Life Sciences and Bioengineering Center at Gateway Park has developed a new model system to study fungal infections.
Technique finds gene regulatory sites without knowledge of regulators
A new statistical technique developed by researchers at the University of Illinois allows scientists to scan a genome for specific gene-regulatory regions without requiring prior knowledge of the relevant transcription factors.
Causative gene of a rare disorder discovered by sequencing only protein-coding regions of genome
For the first time, scientists have successfully used a method called exome sequencing to quickly discover a previously unknown gene responsible for a mendelian disorder.
New research into the mechanisms of gene regulation
A team led by Penn State's Ross Hardison, T. Ming Chu Professor of Biochemistry and Molecular Biology, has taken a large step toward unraveling how regulatory proteins control the production of gene products during development and growth.
Maize cell wall genes identified, giving boost to biofuel research
Purdue University scientists have helped identify and group the genes thought to be responsible for cell wall development in maize, an effort that expands their ability to discover ways to produce the biomass best suited for biofuels production.
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