First analysis of tumor-suppressor interactions with whole genome in normal human cells reveals key differences with cancer cells

ScienceDaily (Nov. 30, 2011) — Scientists investigating the interactions, or binding patterns, of a major tumor-suppressor protein known as p53 with the entire genome in normal human cells have turned up key differences from those observed in cancer cells. The distinct binding patterns reflect differences in the chromatin (the way DNA is packed with proteins), which may be important for understanding the function of the tumor suppressor protein in cancer cells.

The study was conducted by scientists at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory and collaborators at Cold Spring Harbor Laboratory, and is published in the December 15 issue of the journal Cell Cycle.

"No other study has shown such a dramatic difference in a tumor suppressor protein binding to DNA between normal and cancer-derived cells," said Brookhaven biologist Krassimira Botcheva, lead author on the paper. "This research makes it clear that it is essential to study p53 functions in both types of cells in the context of chromatin to gain a correct understanding of how p53 tumor suppression is affected by global epigenetic changes -- modifications to DNA or chromatin -- associated with cancer development."

Because of its key role in tumor suppression, p53 is the most studied human protein. It modulates a cell's response to a variety of stresses (nutrient starvation, oxygen level changes, DNA damage caused by chemicals or radiation) by binding to DNA and regulating the expression of an extensive network of genes. Depending on the level of DNA damage, it can activate DNA repair, stop the cells from multiplying, or cause them to self-destruct -- all of which can potentially prevent or stop tumor development. Malfunctioning p53 is a hallmark of human cancers.

Most early studies of p53 binding explored its interactions with isolated individual genes, and all whole-genome studies to date have been conducted in cancer-derived cells. This is the first study to present a high-resolution genome-wide p53-binding map for normal human cells, and to correlate those findings with the "epigenetic landscape" of the genome.

"We analyzed the p53 binding in the context of the human epigenome, by correlating the p53 binding profile we obtained in normal human cells with a published high-resolution map of DNA methylation -- a type of chemical modification that is one of the most important epigenetic modifications to DNA -- that had been generated for the same cells," Botcheva said.

Key findings

In the normal human cells, the scientists found p53 binding sites located in close proximity to genes and particularly at the sites in the genome, known as transcriptions start sites, which represent "start" signals for transcribing the genes. Though this association of binding sites with genes and transcription start sites was previously observed in studies of functional, individually analyzed binding sites, it was not seen in high-throughput whole-genome studies of cancer-derived cell lines. In those earlier studies, the identified p53 binding sites were found not close to genes, and not close to the sites in the human genome where transcription starts.

Additionally, nearly half of the newly identified p53 binding sites in the normal cells (in contrast to about five percent of the sites reported in cancer cells) reside in so-called CpG islands. These are short DNA sequences with unusually high numbers of cytosine and guanine bases (the C and G of the four-letter genetic code alphabet, consisting of A, T, C, and G). CpG islands tend to be hypo- (or under-) methylated relative to the heavily methylated mammalian genome.

"This association of binding sites with CpG islands in the normal cells is what prompted us to investigate a possible genome-wide correlation between the identified sites and the CpG methylation status," Botcheva said.

The scientists found that p53 binding sites were enriched at hypomethylated regions of the human genome, both in and outside CpG islands.

"This is an important finding because, during cancer development, many CpG islands are subjected to extensive methylation while the bulk of the genomic DNA becomes hypomethylated," Botcheva said. "These major epigenetic changes may contribute to the differences observed in the p53-binding-sites' distribution in normal and cancer cells."

The scientists say this study clearly illustrates that the genomic landscape -- the DNA modifications and the associated chromatin changes -- have a significant effect on p53 binding. Furthermore, it greatly extends the list of experimentally defined p53 binding sites and provides a general framework for investigating the interplay between transcription factor binding, tumor suppression, and epigenetic changes associated with cancer development.

This research, which was funded by the DOE Office of Science, lays groundwork for further advancing the detailed understanding of radiation effects, including low-dose radiation effects, on the human genome.

The research team also includes John Dunn and Carl Anderson of Brookhaven Lab, and Richard McCombie of Cold Spring Harbor Laboratory, where the high-throughput Illumina sequencing was done.

Methodology

The p53 binding sites were identified by a method called ChIP-seq: for chromatin immunoprecipitation (ChIP), which produces a library of DNA fragments bound by a protein of interest using immunochemistry tools, followed by massively parallel DNA sequencing (seq) for determining simultaneously millions of sequences (the order of the nucleotide bases A, T, C and G in DNA) for these fragments.

"The experiment is challenging, the data require independent experimental validation and extensive bioinformatics analysis, but it is indispensable for high-throughput genomic analyses," Botcheva said. Establishing such capability at BNL is directly related to the efforts for development of profiling technologies for evaluating the role of epigenetic modifications in modulating low-dose ionizing radiation responses and also applicable for plant epigenetic studies.

The analysis required custom-designed software developed by Brookhaven bioinformatics specialist Sean McCorkle.

"Mapping the locations of nearly 20 million sequences in the 3-billion-base human genome, identifying binding sites, and performing comparative analysis with other data sets required new programming approaches as well as parallel processing on many CPUs," McCorkle said. "The sheer volume of this data required extensive computing, a situation expected to become increasingly commonplace in biology. While this work was a sequence data-processing milestone for Brookhaven, we expect data volumes only to increase in the future, and the computing challenges to continue."

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by DOE/Brookhaven National Laboratory.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal References:

Krassimira Botcheva, Sean R. McCorkle, W.R. McCombie, John J. Dunn, Carl W. Anderson. Distinct p53 genomic binding patterns in normal and cancer-derived human cells. Cell Cycle, 2011; 10 (24) [link]William A. Freed-Pastor, Carol Prives. Dissimilar DNA binding by p53 in normal and tumor-derived cells. Cell Cycle, 2011; 10 (24) [link]

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Read More

Gene is first linked to herpes-related cold sores

ScienceDaily (Nov. 30, 2011) — A team of researchers from the University of Utah and the University of Massachusetts has identified the first gene associated with frequent herpes-related cold sores.

The findings were published in the Dec. 1, 2011, issue of the Journal of Infectious Diseases.

Herpes simplex labialis (HSL) is an infection caused by herpes simplex virus type 1 (HSV-1) that affects more than 70 percent of the U.S. population. Once HSV-1 has infected the body, it is never removed by the immune system. Instead, it is transported to nerve cell bodies, where it lies dormant until it is reactivated. The most common visible symptom of HSV-1 reactivation is a cold sore on or around the mouth. Although a majority people are infected by HSV-1, the frequency of cold sore outbreaks is extremely variable and the causes of reactivation are uncertain.

"Researchers believe that three factors contribute to HSV-1 reactivation -- the virus itself, exposure to environmental factors, and genetic susceptibility," says John D. Kriesel, M.D., research associate professor of infectious diseases at the University of Utah School of Medicine and first author on the study. "The goal of our investigation was to define genes linked to cold sore frequency."

Kriesel and his colleagues previously had identified a region of chromosome 21 containing six genes significantly linked to HSL disease using DNA collected from 43 large families to map the human genome. In the current study, Kriesel and his colleagues performed intensive analysis of this chromosome region using single nucleotide polymorphism (SNP) genotyping, a test which identifies differences in genetic make-up between individuals.

"Using SNP genotyping, we were able to identify 45 DNA sequence variations among 618 study participants, 355 of whom were known to be infected with HSV-1," says Kriesel. "We then used two methods called linkage analysis and transmission disequilibrium testing to determine if there was a genetic association between particular DNA sequence variations and the likelihood of having frequent cold sore outbreaks."

Kriesel and his colleagues discovered that an obscure gene called C21orf91 was associated with susceptibility to HSL. They identified five major variations of C21orf91, two of which seemed to protect against HSV-1 reactivation and two of which seemed to increase the likelihood of having frequent cold sore outbreaks.

"There is no cure for HSV-1 and, at this time, there is no way for us to predict or prevent cold sore outbreaks," says Kriesel. "The C21orf91 gene seems to play a role in cold sore susceptibility, and if this data is confirmed among a larger, unrelated population, this discovery could have important implications for the development of drugs that affect cold sore frequency."

Kriesel's University of Utah collaborators include Maurine R. Hobbs, Ph.D., research assistant professor of internal medicine and adjunct assistant professor of human genetics, and Mark F. Leppert, Ph.D., distinguished professor and former chair of human genetics.

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by University of Utah Health Sciences.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

J. D. Kriesel, B. B. Jones, N. Matsunami, M. K. Patel, C. A. St. Pierre, E. A. Kurt-Jones, R. W. Finberg, M. Leppert, M. R. Hobbs. C21orf91 Genotypes Correlate With Herpes Simplex Labialis (Cold Sore) Frequency: Description of a Cold Sore Susceptibility Gene. Journal of Infectious Diseases, 2011; 204 (11): 1654 DOI: 10.1093/infdis/jir633

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Read More

World's first captive breeding of Ozark hellbenders

ScienceDaily (Dec. 1, 2011) — Ozark hellbenders have been bred in captivity -- a first for either of the two subspecies of hellbender. The decade-long collaboration of the Saint Louis Zoo's Ron Goellner Center for Hellbender Conservation and the Missouri Department of Conservation has yielded 63 baby hellbenders.

The first hellbender hatched on Nov. 15, and currently there are approximately 120 additional eggs that should hatch within the next week. The eggs are maintained in climate- and water quality-controlled trays behind the scenes in the Zoo's Herpetarium. For 45 to 60 days after emerging, the tiny larvae will retain their yolk sack for nutrients and move very little as they continue their development. As the larvae continue to grow, they will develop legs and eventually lose their external gills by the time they reach 1.5 to 2 years of age. At sexual maturity, at 5 to 8 years of age, adult lengths can approach two feet. Both parents are wild bred: the male has been at the Zoo for the past two years and the female arrived this past September.

Rivers in south-central Missouri and adjacent Arkansas once supported up to 8,000 Ozark hellbenders. Today, fewer than 600 exist in the world-so few that the amphibian was added in October 2011 to the federal endangered species list.

Due to these drastic declines, captive propagation became a priority in the long-term recovery of the species. Once the captive-bred larvae are 3 to 8 years old, they can then be released into their natural habitat-the Ozark aquatic ecosystem.

Also known by the colloquial names of "snot otter" and "old lasagna sides," the adult hellbender is one of the largest species of salamanders in North America, with its closest relatives being the giant salamanders of China and Japan, which can reach five feet in length.

With skin that is brown with black splotches, the Ozark hellbender has a slippery, flattened body that moves easily through water and can squeeze under rocks on the bottom of streams.

Like a Canary in a Coal Mine

Requiring cool, clean running water, the Ozark hellbender is also an important barometer of the overall health of that ecosystem-an aquatic "canary in a coal mine."

"Capillaries near the surface of the hellbender's skin absorb oxygen directly from the water -- as well as hormones, heavy metals and pesticides," said Jeff Ettling, Saint Louis Zoo curator of herpetology and aquatics. "If there is something in the water that is causing the hellbender population to decline, it can also be affecting the citizens who call the area home."

"We have a 15- to 20-year window to reverse this decline," added Missouri Department of Conservation Herpetologist Jeff Briggler, who cites a number of reasons for that decline from loss of habitat to pollution to disease to illegal capture and overseas sale of the hellbender for pets. "We don't want the animal disappearing on our watch."

Reversing A Decline

In 2001, the Ozark Hellbender Working Group of scientists from government agencies, public universities and zoos in Missouri and Arkansas launched a number of projects to staunch that decline. These included egg searches, disease sampling and behavioral studies.

In 2004, funding from private donors, the Missouri Department of Conservation, the United States Fish & Wildlife Services and the Zoo covered the cost of building sophisticated facilities including climate-controlled streams to breed the hellbender.

The hellbender propagation facilities include two outdoor streams that are 40 feet long and six feet deep. The area is landscaped with natural gravel, large rocks for hiding and artificial nest boxes, where the fertilized eggs were discovered. A nearby building houses state-of-the-art life support equipment used to filter the water and maintain the streams at the proper temperature.

In addition, two large climate-controlled rooms in the basement of the Zoo's Charles H. Hoessle Herpetarium are the headquarters for the program. The facilities recreate hellbender habitat with closely monitored temperatures, pumps to move purified water, sprinklers synced to mimic the exact precipitation and lights that flick on or dim to account for brightness and shade. The largest room includes a 32-foot simulated stream, complete with native gravel and large rocks for hiding. It houses a breeding group of adult Ozark hellbenders from the North Fork of the White River in Missouri; offspring from these hellbenders will eventually be released back into the wild.

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by Saint Louis Zoo.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Read More

Trail of 'stone breadcrumbs' reveals the identity of one of the first human groups to leave Africa

ScienceDaily (Nov. 30, 2011) — A series of new archaeological discoveries in the Sultanate of Oman, nestled in the southeastern corner of the Arabian Peninsula, reveals the timing and identity of one of the first modern human groups to migrate out of Africa, according to a research article published in the open-access journal PLoS ONE.

An international team of archaeologists and geologists working in the Dhofar Mountains of southern Oman, led by Dr. Jeffrey Rose of the University of Birmingham, report finding over 100 new sites classified as "Nubian Middle Stone Age (MSA)." Distinctive Nubian MSA stone tools are well known throughout the Nile Valley; however, this is the first time such sites have ever been found outside of Africa. According to the authors, the evidence from Oman provides a "trail of stone breadcrumbs" left by early humans migrating across the Red Sea on their journey out of Africa. "After a decade of searching in southern Arabia for some clue that might help us understand early human expansion, at long last we've found the smoking gun of their exit from Africa," says Rose. "What makes this so exciting," he adds, "is that the answer is a scenario almost never considered." These new findings challenge long-held assumptions about the timing and route of early human expansion out of Africa.

Using a technique called Optically Stimulated Luminescence (OSL) to date one of the sites in Oman, researchers have determined that Nubian MSA toolmakers had entered Arabia by 106,000 years ago, if not earlier. This date is considerably older than geneticists have put forth for the modern human exodus from Africa, who estimate the dispersal of our species occurred between 70,000 and 40,000 years ago. Even more surprising, all of the Nubian MSA sites were found far inland, contrary to the currently accepted theory that envisions early human groups moving along the coast of southern Arabia. "Here we have an example of the disconnect between theoretical models versus real evidence on the ground," says co-author Professor Emeritus Anthony Marks of Southern Methodist University. "The coastal expansion hypothesis looks reasonable on paper, but there is simply no archaeological evidence to back it up.

Genetics predict an expansion out of Africa after 70,000 thousand years ago, yet we've seen three separate discoveries published this year with evidence for humans in Arabia thousands, if not tens of thousands of years prior to this date." The presence of Nubian MSA sites in Oman corresponds to a wet period in Arabia's climatic history, when copious rains fell across the peninsula and transformed its barren deserts to sprawling grasslands. "For a while," remarks Rose, "South Arabia became a verdant paradise rich in resources -- large game, plentiful freshwater, and high-quality flint with which to make stone tools." Far from innovative fishermen, it seems that early humans spreading from Africa into Arabia were opportunistic hunters traveling along river networks like highways. Whether or not these pioneers were able to survive in Arabia during the hyperarid conditions of the Last Ice Age is another matter -- a mystery that will require archaeologists to continue combing the deserts of southern Arabia, hot on the trail of stone breadcrumbs.

The Dhofar Archaeological Project is conducted under the auspices of the Ministry of Heritage and Culture in Oman. The team is composed of an interdisciplinary group of researchers from the University of Birmingham and Oxford Brookes University, UK; Arizona State University and Southern Methodist University, USA; Institute of Archaeology, National Academy of Sciences, Ukraine; Institute of Archaeology of the Academy of Science, Czech Republic; University of Tübingen, Germany, and the University of Wollongong, Australia. The project is funded by research grants from the UK Arts and Humanities Research Council and the Australian Research Council.

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by Public Library of Science.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Jeffrey I. Rose, Vitaly I. Usik, Anthony E. Marks, Yamandu H. Hilbert, Christopher S. Galletti, Ash Parton, Jean Marie Geiling, Viktor Cerný, Mike W. Morley, Richard G. Roberts. The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia. PLoS ONE, 2011; 6 (11): e28239 DOI: 10.1371/journal.pone.0028239

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Read More

Scientists measure dream content for the first time: Dreams activate the brain in a similar way to real actions

ScienceDaily (Oct. 28, 2011) — The ability to dream is a fascinating aspect of the human mind. However, how the images and emotions that we experience so intensively when we dream form in our heads remains a mystery. Up to now it has not been possible to measure dream content. Max Planck scientists working with colleagues from the Charité hospital in Berlin have now succeeded, for the first time, in analysing the activity of the brain during dreaming.

They were able to do this with the help of lucid dreamers, i.e. people who become aware of their dreaming state and are able to alter the content of their dreams. The scientists measured that the brain activity during the dreamed motion matched the one observed during a real executed movement in a state of wakefulness.

The research is published in the journal Current Biology.

Methods like functional magnetic resonance imaging have enabled scientists to visualise and identify the precise spatial location of brain activity during sleep. However, up to now, researchers have not been able to analyse specific brain activity associated with dream content, as measured brain activity can only be traced back to a specific dream if the precise temporal coincidence of the dream content and measurement is known. Whether a person is dreaming is something that could only be reported by the individual himself.

Scientists from the Max Planck Institute of Psychiatry in Munich, the Charité hospital in Berlin and the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig availed of the ability of lucid dreamers to dream consciously for their research. Lucid dreamers were asked to become aware of their dream while sleeping in a magnetic resonance scanner and to report this "lucid" state to the researchers by means of eye movements. They were then asked to voluntarily "dream" that they were repeatedly clenching first their right fist and then their left one for ten seconds.

This enabled the scientists to measure the entry into REM sleep -- a phase in which dreams are perceived particularly intensively -- with the help of the subject's electroencephalogram (EEG) and to detect the beginning of a lucid phase. The brain activity measured from this time onwards corresponded with the arranged "dream" involving the fist clenching. A region in the sensorimotor cortex of the brain, which is responsible for the execution of movements, was actually activated during the dream. This is directly comparable with the brain activity that arises when the hand is moved while the person is awake. Even if the lucid dreamer just imagines the hand movement while awake, the sensorimotor cortex reacts in a similar way.

The coincidence of the brain activity measured during dreaming and the conscious action shows that dream content can be measured. "With this combination of sleep EEGs, imaging methods and lucid dreamers, we can measure not only simple movements during sleep but also the activity patterns in the brain during visual dream perceptions," says Martin Dresler, a researcher at the Max Planck Institute for Psychiatry.

The researchers were able to confirm the data obtained using MR imaging in another subject using a different technology. With the help of near-infrared spectroscopy, they also observed increased activity in a region of the brain that plays an important role in the planning of movements. "Our dreams are therefore not a 'sleep cinema' in which we merely observe an event passively, but involve activity in the regions of the brain that are relevant to the dream content," explains Michael Czisch, research group leader at the Max Planck Institute for Psychiatry.

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by Max-Planck-Gesellschaft.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Martin Dresler, Stefan P. Koch, Renate Wehrle, Victor I. Spoormaker, Florian Holsboer, Axel Steiger, Philipp G. Sämann, Hellmuth Obrig, Michael Czisch. Dreamed Movement Elicits Activation in the Sensorimotor Cortex. Current Biology, Published online Oct. 27, 2011 DOI: 10.1016/j.cub.2011.09.029

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Read More