Stem cell researchers from UCLA used a high resolution technique to examine the genome, or total DNA content, of a pair of human embryonic stem cell lines and found that while both lines could form neurons, the lines had differences in the numbers of certain genes that could control such things as individual traits and disease susceptibility. The technique used to study the genome, which contains all the genes on 46 chromosomes, is called array CGH. The use of higher resolution techniques, such as array CGH and, soon, whole genome sequencing, will enhance the ability of researchers to examine stem cell lines to determine which are best – least likely to result in diseases and other problems – to use in creating therapies for use in humans.

Array CGH provided a much better look at the gene content on the chromosomes of human embryonic stem cells, with a resolution about 100 times better than standard clinical methods. Clinical specialists commonly generate a karyotype to examine the chromosomes of cancer cells or for amniocentesis in prenatal diagnosis, which has a much lower resolution than Array CGH, said Michael Teitell, a researcher with the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and the senior author of the study. Small defects that could result in big problems later on could be missed using karyotyping for stem cells.

“Basically, this study shows that the genetic makeup of individual human embryonic stem cell lines is unique in the numbers of copies of certain genes that may control traits and things like disease susceptibility,” said Teitell, who also is an associate professor of pathology and laboratory medicine and a researcher at UCLA’s Jonsson Comprehensive Cancer Center. “So, in choosing stem cell lines to use for therapeutic applications, you want to know about these differences so you don’t pick a line likely to cause problems for a patient receiving these cells.”

The study appears in the March 27, 2008 express edition of the journal Stem Cells.

Differences between individual DNA sequences provide the basis for human genetic variability. Forms of variation include single DNA base pair alterations, duplications or deletions of genes or sets of genes, and translocations, a chromosomal rearrangement in which a segment of genetic material from one chromosome becomes heritably linked to another chromosome. These changes can be benign, but they can also promote diseases such as certain cancers, or confer increased risk to other diseases, such as HIV infection or certain types of kidney ailments.

In this study, Teitell and his team sought to determine copy number variants (CNVs), or differences in the numbers of certain genes, in two embryonic stem cell lines. The CNVs provide a unique genetic fingerprint for each line, which can also indicate relatedness between any two stem cell lines. Teitell used embryonic stem cell lines that made different types of neurons and studied them with array CGH for comparison. His team found CNV differences between the two lines in at least seven different chromosome locations below the level of detection using standard karyotype studies. Such differences could impact the therapeutic utility of the lines and could have implications in disease development. More studies will be required to determine the effect of specific CNVs in controlling stem cell function and disease susceptibility, he said.

“In studying embryonic stem cell lines in the future, if we find differences in regions of the genome that we know are associated with certain undesirable traits or diseases, we would choose against using such stem cells, provided safer alternative lines are available,” Teitell said.

Large genome-wide association studies are underway in a variety of diseases to determine what genetic abnormalities might be at play. When the genetic fingerprint or predisposing genes for a certain disease is discovered, it could be used as key information in screening embryonic stem cell lines.

According to researchers at Temple University an increase in the CD163+/CD16+ monocyte subset could be a biomarker for the progression of HIV disease.The researchers reported their findings, “CD163/CD16 Coexpression by Circulating Monocytes/Macrophages in HIV: Potential Biomarkers for HIV Infection and AIDS Progression,” in the March issue of AIDS Research and Human Retroviruses (www.liebertonline.com/aid).

A monocyte is a specific white blood cell, a part of the human body’s immune system that protects against blood-borne pathogens and moves quickly to sites of infection within the body’s tissues. As monocytes enter tissue, they undergo a series of changes to become macrophages.

The researchers were investigating alterations in this monocyte subset in patients with HIV infection. As part of this study, they examined a cohort of 18 patients from the Comprehensive HIV Program at Temple University Hospital, under the direction of Ellen Tedaldi, and seven individuals without HIV infection.

“At first, we were just looking at whether or not we saw alterations in this CD163+/CD16+ subset and whether it might be reflective of the amount of virus they have in circulation,” said Tracy Fischer-Smith, an associate scientist in Temple’s Neuroscience Department and the study’s lead author. “We did, indeed, find that patients with detectable virus had an increase of this monocyte subset that correlated with the amount of virus they had in their blood. We were surprised to find that patients with CD4+ T cell counts of less than 450 cells per microliter [200 or less per microliter is defined as AIDS], the increase of this monocyte subset correlates inversely with the number of T cells.”

Fischer-Smith said this finding suggests that as the monocyte cells are increasing, these patients are losing CD4+ T cells, which are critical for the maintenance of immunological competence.

“This may actually provide an earlier window into what is happening with HIV-infected patients where we might be able to see that immune impairment is taking place before we see a dramatic loss of CD4+ T cells,” she said.

“It looks like, based on these correlations, that this particular cell type may be involved in immune impairment and the progression of HIV,” said Jay Rappaport, professor of neuroscience and neurovirology, who oversaw the study. “Is it a good prognostic indicator” If you have a lot of these monocytes, does it mean you are going to progress into AIDS faster” “Right now, all we know is what the correlations are,” he said.

Rappaport added that he believes the CD163+/CD16+ monocyte subset is the first biomarker that correlates with viral load and CD4+ count. “The fact that it actually correlates with both, we think, might make it a key cell type in the pathogenesis of AIDS.” Fischer-Smith said the researchers plan to expand this study by following a cohort of patients longitudinally to see if their findings really can provide doctors with an early warning system and help to design better therapeutic strategies.

“When you are just looking at a single time-point, you don’t know how changes in this monocyte subset might occur over time, and how these changes might relate to the viral load and T cell number in individual patients,” she said. “That is why we want to investigate this further with a longitudinal study of HIV patients.”

The study was supported by the National Institute of Neurological Disorders and Strokes (NINDS) and the National Institute on Drug Abuse (NIDA)

CHESTNUT HILL, MA – It took a global corps of scientists approximately $500 million and 13 years to identify the more than 35,000 genes of the human genome. Five years later, Boston College Biologist Gabor Marth and his research team have developed software that can analyze half a million DNA sequences in 10 minutes.The Marth laboratory’s proprietary PyroBayes software is one of a new breed of computer programs able to accurately process the mountains of genome data flowing from the latest generation of gene decoding machines, which have placed a premium on computational speed and accuracy in data-crunching fields known as bioinformatics and high-throughput biology, said Marth, an associate professor of Biology.

“We’re on the edge of a real technological revolution that I think will help us understand the genetic causes of diseases in humans and how genetic materials determine traits in animals,” said Marth. “It is going to lead to less expensive technologies that will allow researchers to decode any individual.”

PyroBayes will aid researchers involved in the 1,000 Genomes Project, which announced last month a plan to sequence the genomes of 1,000 individuals from around the world. The NIH, which helps direct the project, has awarded Marth more than $1.3 million to develop software over the next four years.

The advances of the Marth lab were revealed in two articles published by the professor and his assistants in the February issue of Nature Methods, the premier journal of scientific research methodology.

In an article co-authored by Marth, post-doctoral researcher Chip Stewart, and graduate students Aaron Quinlan and Mike Strömberg, the group unveiled the lab’s PyroBayes base caller software, which examines data from one of the latest generation of DNA decoding machines – from Roche / 454 Life Sciences – faster and with far greater accuracy than other programs for pyrosequencing, a technology that utilizes the detection of pyrophosphate for decoding the sequence of DNA, the carrier of genetic information in living organisms.

A second Nature Methods article, written in collaboration with colleagues from the Washington University School of Medicine, reported that three other computer programs developed by the Marth lab made it possible to quickly and accurately examine the whole genome of a laboratory worm and identify key differences between the sample strain and an earlier strain – a comparative process known as re-sequencing, now being applied to the genomes of humans and other organisms. This second study used another next-generation DNA sequencing platform, the Illumina/Solexa machine.

Advances are driving re-sequencing costs down, but researchers must still prove the effectiveness of the new technology by working with smaller organisms, which made the worm study critical, Marth said. “This brings us closer to a major milestone in human individual re-sequencing – the decoding of the genome of human beings in routine fashion,” said Marth.

Of the few computer programs available for the new sequencing machines, the software package developed by the Marth lab is the only one capable of working with a variety of decoding machines and offers greater accuracy, allowing researchers to separate true genetic variations from data errors, said Marth. PyroBayes, a Linux-based package, is made available to fellow academic researchers at no cost.

As a member of its analysis group, the Marth lab participates in the data analysis of the 1000 Genomes Project, which was launched last month. The goal of the project is to sequence the genomes of at least 1,000 people from around the world to create the most detailed and medically useful picture to date of human genetic variation.

Ultimately, advances in bioinformatics will help push genetic science forward, shedding new light on human health and disease. Marth sees his lab’s role in providing critical tools that help researchers to organize data, interpret them, and visualize genome variations.

“We are excited to develop the software that will help these super-fast, high-throughput sequencing machines to realize their potential to produce invaluable data for research,” Marth said.

Nature Methods: http://www.nature.com/nmeth/journal/v5/n2/full/nmeth.1172.html.

Today, scientists know more now than ever before about the microbes that inhabit our mouths. They know so much, in fact, that gathering all of the relevant bits of information into one place when designing experiments can be a job in itself. Now, grantees of the National Institute of Dental and Craniofacial Research (NIDCR), part of the National Institutes of Health, and their international colleagues intend to solve this problem with the launch of the first comprehensive database of the oral microbiome, or the approximately 600 distinct microorganisms currently known to live in the mouth.The free online compendium is called the Human Oral Microbiome Database (HOMD). The database goes live today as the digital equivalent of an Oxford dictionary of oral microorganisms, providing detailed biological entries for each species and an extensive catalogue of the thousands of genes that these microbes express. The site is located at http://www.homd.org and is overseen by scientists at The Forsyth Institute in Boston and King’s College London in England.

“The HOMD fills a critical research need,” said NIDCR director Lawrence Tabak, D.D.S., Ph.D. “The oral microbiome is extremely rich in data, and HOMD becomes the essential search engine for scientists to view and retrieve this information, generate novel hypotheses, make computational discoveries, and ultimately develop more biologically sound therapies to control oral diseases.”

According to Floyd Dewhirst, D.D.S., Ph.D., a leader of the project and a scientist at The Forsyth Institute, HOMD also introduces the first comprehensive nomenclature system to bring order to the naming of uncultured or previously unnamed oral microbes. The standardized numbering system helps to eliminate the Babel of confusing names and uninformative database designations that have frustrated scientists and sometimes hindered their research.

The database also categorizes each microbe by its 16S rRNA sequence, a distinctive fingerprint of genetic information that scientists have used for the past two decades to identify microorganisms. This sequence information allows the microbes to be placed in a family tree that shows how they are related to one another. For those organisms whose DNA has been sequenced, HOMD provides online tools to view and analyze all of their genes and proteins. Each category of information in the database is interlinked, readily searchable, appropriately annotated, and will be frequently updated to remain current.

Dewhirst noted that although HOMD has officially opened to scientists, the database remains an ongoing project. “We’ve already assembled a great deal of useful information for the research community, but we will continue to expand and refine the database for the next several years,” said Dewhirst. “I can see the Human Oral Microbiome Database serving as a valuable model for other microbiome databases now and in the years to come.”

Informally called “biology’s next revolution,” microbiome studies have opened a needed window into the complex microbial communities that occupy most parts of the human body. These studies will define how microbes contribute to sustaining health and, when their community dynamics are perturbed, play a role in common chronic disease, such as tooth decay and periodontal disease in the mouth. In December 2007, NIH launched the Human Microbiome Project that initially will sequence all of the genes, or genomes, of 600 representative microorganisms sampled from microbial communities in the mouth, skin, digestive tract, nose, and female urogenital tract. Additional studies are either under way or under development.

Among those already well under way is a NIDCR-supported project to compile a full catalogue of the complete genomes of all oral microbes. It has generated a tremendous amount of data and, coupled with the decades of more traditional studies of oral bacteria, the need for a comprehensive, user-friendly database has become a priority.

“The oral microbiome is currently better understood than those of other sites in the body, such as the intestine,” said Dr. Bruce Paster, Ph.D., also at The Forsyth Institute and another project scientist. “Since oral microorganisms appear in infections throughout the human body, the HOMD database certainly will be useful to physicians. Likewise, microbiologists in industry will find HOMD helpful because oral microbes sometimes contaminate food or the drug manufacturing process.”

The National Institute of Dental and Craniofacial Research (NIDCR) is the Nation’s leading funder of research on oral, dental, and craniofacial health.

Shown is an image of bacteriophage Epsilon15 studied by Wen Jiang, an assistant professor of biological sciences at Purdue. The bacteriophage is shown at a resolution of 4.5 angstrom — the highest resolution achieved for a living organism of this size. Credit Graphic/Wen Jiang lab

WEST LAFAYETTE, Ind. - A team led by a Purdue University researcher has achieved images of a virus in detail two times greater than had previously been achieved.

Wen Jiang, an assistant professor of biological sciences at Purdue, led a research team that used the emerging technique of single-particle electron cryomicroscopy to capture a three-dimensional image of a virus at a resolution of 4.5 angstroms. Approximately 1 million angstroms would equal the diameter of a human hair.

“This is one of the first projects to refine the technique to the point of near atomic-level resolution,” said Jiang, who also is a member of Purdue’s structural biology group. “This breaks a threshold and allows us to now see a whole new level of detail in the structure. This is the highest resolution ever achieved for a living organism of this size.”

Details of the structure of a virus provide valuable information for development of disease treatments, he said.

“If we understand the system - how the virus particles assemble and how they infect a host cell - it will greatly improve our ability to design a treatment,” Jiang said. “Structural biologists perform the basic science and provide information to help those working on the clinical aspects.”

A paper detailing the work was published in the Feb. 28 issue of Nature.

Roger Hendrix, a professor of biological sciences at the University of Pittsburgh, said what is learned about viruses can be applied to many other biological systems.

“Understanding the proteins that create the structure of a virus gives us insight into the tiny biological machines found throughout our bodies,” he said. “Getting to 4.5 angstrom using this technique is a watershed of sorts because it is the first time we can actually trace the polypeptide chain - the backbone of proteins. Now we can see the tiny gears and levers that allow the proteins to move and interact as they carry out their intricate biological roles.”

The imaging technique, called cryo-EM, has the added benefit of maintaining the sample being studied in a state very similar to its natural environment. Other imaging techniques used regularly, such as X-ray crystallography, require the sample be manipulated.

“This method offers a new approach for modeling the structure of proteins in other macromolecular assemblies, such as DNA, at near-native states,” Jiang said. “The sample is purified in a solution that is very similar to the environment that would be found in a host cell. It is as if the virus is frozen in glass and it is alive and infectious while we examine it.”

In addition to Jiang, Matthew L. Baker, Joanita Jakana and Wah Chiu from Baylor College of Medicine, and Peter R. Weigele and Jonathan King from Massachusetts Institute of Technology worked on the project, which was funded by the National Institutes of Health and the National Science Foundation.

The team obtained a three-dimensional map of the capsid, or protein shell, of the epsilon15 bacteriophage, a virus that infects bacteria and is a member of a family of viruses that are the most abundant life forms on Earth, Jiang said.

Other methods of determining the structure could not be used for this family of virus. None had been successfully crystallized, and the complexity of members of this family had prevented evaluation through the genome sequence alone.

“This demonstration shows that cryo-EM is doable and is a major step in reaching the full potential of this technique,” he said. “The goal is to have it reach a 3 to 4 angstrom resolution, which would allow us to clearly see the amino acids that make up a protein.”

In electron microscopy, a beam of electrons takes the place of the light beam used in a conventional microscope. The use of electrons instead of light allows the microscope to “see” in much greater detail.

Cryo-EM cools specimens to temperatures well below the freezing point of water. This decreases damage from the electron beam and allows the specimens to be examined for a longer period of time. Longer exposure time allows for sharper, more detailed images.

Researchers using cryo-EM had obtained images at a resolution of 6-9 angstroms but could not differentiate between smaller elements of the structure spaced only 4.5 angstroms apart.

“There are different elements that make up the protein building blocks of the virus,” Jiang said. “It is like examining a striped blanket. From a distance, the stripes blur together and the blanket appears to be one solid color. As you get closer you can see the different stripes, and if you use a magnifying glass you can see the strands of string that make up the material. The resolution needs to be smaller than the distance between the strands of thread in order to see two separate strands.

“By being able to zoom in, researchers were able to see components that blurred together at the earlier achieved resolution.”

Cryo-EM requires high-end electron microscopes and powerful computing resources. The research team used the Baylor College of Medicine’s cryoelectron microscope. It is expected that Purdue will install a state-of-the-art cryoelectron microscope in 2009.

In 2006 Purdue received a $2 million grant from the National Institute of Health to purchase the microscope. It will be installed in Hockmeyer Hall of Structural Biology, expected to open in 2009.

Computer programs are used to extract the signal from the microscope and to combine thousands of two-dimensional images into an accurate three-dimensional image that maps the structure of the virus. This requires use of a large data set and could not have been done without the resources of Purdue’s Office of Information Technology, or ItaP, Jiang said.

Jiang used Purdue’s Condor program - which links computers including desktop machines and large, powerful research computers - to create the largest distributed computing network at a university.

“ITaP provided us with computational power at the supercomputer scale that was necessary for this work,” he said. “Purdue’s Condor program allowed us to take advantage of the power of 7,000 computers. This was a critical element to our success.”

Jiang plans to continue to refine every step of the process to improve the capabilities of the technique and to examine more medically relevant virus species.

Purdue’s structural biology group studies a diverse group of problems, including cellular signaling pathways, RNA catalysis, bioremediation, molecular evolution, viral entry, viral replication and viral pathogenesis. Researchers use a combination of X-ray crystallography, electron cryomicroscopy, NMR spectroscopy, and advanced computational and modeling tools to study these problems.

Illinois postdoctoral researcher Feng-Jie Sun (left) and crop sciences professor Gustavo Caetano-Anollés began with the idea that understanding the structural properties of tRNA would shed light on how organisms and viruses evolved. Photo by L. Brian Stauffer, U. of I. News Bureau.

Transfer RNA (also called tRNA) is an ancient molecule, central to every task a cell performs and thus essential to all life. A new study from the University of Illinois indicates that it is also a great historian, preserving some of the earliest and most profound events of the evolutionary past in its structure.

The study, co-written by Gustavo Caetano-Anollés, a professor of crop sciences, and postdoctoral researcher Feng-Jie Sun, appears March 7 in PLoS Computational Biology. Caetano-Anollés is an affiliate of the U. of I. Institute for Genomic Biology.

Of the thousands of RNAs so far identified, transfer RNA (tRNA) is the most direct intermediary between genes and proteins. Like many other RNAs (ribonucleic acids), tRNA aids in translating genes into the chains of amino acids that make up proteins. With the help of a highly targeted enzyme, each tRNA molecule recognizes and latches onto a specific amino acid, which it carries into the protein-building machinery. In order to successfully add its amino acid to the end of a growing protein, tRNA must also accurately read a coded segment of messenger RNA, which gives instructions for the exact sequence of amino acids in the protein.

The fact that tRNA is so central to the task of building proteins probably means that it has been around for a long time, Caetano-Anollés said. His inquiry began with a hunch that understanding the structural properties of tRNA would shed light on how organisms and viruses evolved.

“Perhaps in evolution there are things that are so fundamental that they are kept, held onto, for millions or even billions of years,” Caetano-Anollés said. “Those are the fossils, the molecular fossils, that tell us about the past. Therefore, studying these molecules can address fundamental questions in biology and evolution.”

All tRNAs assemble themselves into a shape that, if flattened, resembles a cloverleaf. Patterns in these structures give clues to early evolutionary history. The red areas of the molecule pictured above are the most ancient. Image courtesy of Gustavo Caetano-Anollés.

All tRNAs assemble themselves into a shape that, if flattened, resembles a cloverleaf. The team began by looking for patterns in this cloverleaf structure, using detailed data from hundreds of molecules representing viruses and each of the three superkingdoms of life: archaea, bacteria and eukarya.

The researchers converted all distinguishing features of the individual tRNA cloverleaf structures into coded characters, a process that allowed a computerized search for the most “parsimonious” (that is, the simplest, most probable) tRNA family tree. They conducted the same analysis on the tRNAs of each of the superkingdoms, to see how far these groupings diverged from the overall tree. This comparison allowed them to determine the order in which viruses and each of the superkingdoms diverged.

The new analysis supports an earlier study that suggested that the archaea were the first to arise as an evolutionarily distinguishable group. Archaea are microbes that can survive in boiling acid, near sulfurous ocean vents or in other extreme environments. The earlier study, also led by Caetano-Anollés, analyzed the vast catalog of protein folds – those precisely configured regions in proteins that give them their functionality – as a guidebook to evolutionary history.

“The transfer RNA data matches our earlier data,” Caetano-Anollés said. “This is important because two lines of independent evidence are supporting each other.”

The new analysis also indicates that viruses emerged not long after the archaea, with the superkingdoms eukarya and bacteria following much later – and in that order. This finding may influence the ongoing debate over whether viruses existed prior to, or after, the emergence of living cells, Caetano-Anollés said.

“This supports the idea that viruses arose from the cellular domain,” he said.

BIRMINGHAM, Ala. – A significant drop in abnormal Pap test results happened after girls and women were given a vaccine to prevent cervical cancer, according to a researcher at the University of Alabama at Birmingham (UAB).The findings show the vaccine, named GARDASIL, appears to prevent the development of cell changes that lead to cervical disease, the researcher said.

In testing GARDASIL reduced abnormal Pap test results by 43 percent compared to women not given the vaccine. The 43 percent reduction was for tests that found pre-cancerous changes called high-grade squamous intraepithelial lesions (HSIL) more than three years after women were given the vaccine.

GARDASIL reduced other abnormal Pap results, including milder pre-malignant cell changes, by 16 to 35 percent compared to women not given the vaccine.

While the findings are not definitive that GARDASIL prevents cancer, they do signal the vaccine will spare thousands of women a diagnosis of cell abnormality or malignant changes that may lead to more tests and possibly surgery, said Warner Huh, M.D., associate professor in the UAB Division of Gynecologic Oncology and the doctor chosen to present the data.

“Clearly the vaccine’s benefits include something that can be appreciated by women and daughters fairly quickly,” Huh said. “This is a positive first sign, and it will take many more years to know definitively if the vaccine prevents cancer.”

The findings were presented March 10 at the annual meeting of the Society of Gynecological Oncologists held in Tampa.

The results are a compilation of three separate trials involving more than 18,000 women, ages 16 to 26, in the United States, Europe and Asia. All test subjects had normal Pap smear readings at the start of the trial.

In addition to the drop in unwanted Pap results, the study found invasive procedures like cervical biopsies were performed up to 42 percent less in GARDASIL recipients compared to women not given the vaccine, Huh said.

GARDASIL is approved to fight the human papilloma virus (HPV) strains believed to cause 70 percent of cervical cancers and more than 90 percent of genital warts.

For many unvaccinated women HPV infections clear up naturally without causing any cervical problems, as do many pre-malignant lesions. In other cases, HPV prompts cell changes that can gradually put women at greater risk of cervical cancer.

Nearly 25 million U.S. women between the ages of 14 and 59 are infected with HPV, and the annual cost of screening and treating cervical abnormalities is about $4 billion, according to a statement from the Society of Gynecologic Oncologists. “Dr. Huh’s study concludes that the trials covered in this paper indicate an overall benefit of vaccination,” the society’s statement said.

Human Papillomavirus is the virus responsible for most cases of cervical cancer has a serious weakness which may provide hope for new treatments for the disease.Human Papillomavirus (HPV), a virus which causes several types of cancer but is particularly associated with cervical cancer, has developed clever ways of hiding in the body, but researchers at the University of Leeds have found that its ability to trick the body’s first line of defence leaves it vulnerable to attack from a second defence system.

When viruses enter cells, they produce proteins to assist their growth and replication, and the body’s immune system is programmed to recognise and attack these non-native proteins.

Professor Eric Blair of the University’s Faculty of Biological Sciences and Dr Graham Cook from the Leeds Institute for Molecular Medicine have been specifically looking at one of the proteins produced by HPV, called E7, and have discovered that it suppresses markers on the cell surface, making infected cells much less visible to T cells, one of the body’s key defence systems.

“T cells can normally tell when there are molecules in the body that shouldn’t be there and activate an immune response,” says Professor Blair. “But HPV uses the E7 protein to hide from them. We’ve always known the virus has clever ways of defending itself, but we now know how one of its main defence mechanism works.”

However, in a twist that offers hope for the development of potential new therapies for cervical cancer, Professor Blair and Dr Cook have also discovered that this subterfuge may be the virus’s downfall.

Cells without surface protein markers are targeted by another of the body’s white blood cell armoury, Natural Killer cells - cellular assassins, which when activated, release specialised enzymes into target cells to kill them.

“Despite the body’s valiant efforts to ward off the virus, women are still contracting this awful disease, so there are clearly other mechanisms at work. We need to look at the role of the other components of the virus, to see if they prevent the Natural Killer cells from attacking,” says Professor Blair. “For example, we’ve started examining the contribution of the virus protein E6, which we believe works in partnership with E7. The recent introduction of a vaccine against HPV is an important development in the fight against cervical cancer. However, it may take many years for the vaccine to reduce the number of cases of this cancer and other approaches to eliminating tumour cells need to be discovered.”

This research was funded by Yorkshire Cancer Research, the charity’s Chief Executive, Elaine King commented: “Human Papillomavirus is extremely complex with many mechanisms affecting how it operates. However, through this research we have discovered how the E7 protein works, which is a huge step forward, and will hopefully help us to develop effective ways to combat Human Papillomavirus in the future.”

Frank J. Slack Citation: Cell Cycle (March 15, 2008). Credit Yale University

New Haven, Conn. — A small RNA molecule, known as let-7 microRNA (miRNA), substantially reduced cancer growth in multiple mouse models of lung cancer, according to work by researchers at Yale University and Asuragen, Inc., published in the journal Cell Cycle.

Cancer afflicts 1.5 million people a year in the United States alone, and lung cancer is the most common and deadly form of cancer worldwide. This study indicates a direct role for a miRNA in cancer progression and introduces a new paradigm of using miRNAs as effective therapeutic agents to treat human cancer.

“We believe this is the first report of a miRNA being used to a beneficial effect on any cancer, let alone lung cancers, the deadliest of all cancers worldwide,” said senior author Frank Slack, associate professor of molecular, cellular and developmental biology at Yale.

Slack’s research group initially discovered the let-7 miRNA in C. elegans, a tiny worm used as a model system for studying how organisms develop, grow and age. They went on to show that in humans, let-7 negatively regulates a well-known determinant of human lung cancers, the RAS oncogene.

Mice treated with let-7 show substantially reduced lung tumor load. Sections from lungs of mice with tumors that were untreated (c, d) or treated (a, b) with intranasal dosing of… Citation: Cell Cycle (March 15, 2008). Credit Yale University

In collaboration with scientists at Asuragen, the Slack lab has studied the tumor suppressor activity of this small RNA. Their work revealed that let-7 is commonly present at substantially reduced levels in lung tumors — and that reduced levels of let-7 likely contribute to the development of the tumors. These discoveries focused public attention and research efforts to understand the potential use of naturally occurring microRNAs like let-7 to combat cancer.

This new work demonstrates that let-7 inhibits the growth of lung cancer cells in culture and in lung tumors in mice. They also showed that let-7 can be applied as an intranasal drug to reduce tumor formation in a RAS mouse model lung cancer.

“We believe that our studies provide the first direct evidence in mammals, that let-7 functions as a tumor suppressor gene,” said Slack. “Because multiple cell lines and mouse models of lung cancer were used, it appears that therapeutic application of let-7 may provide benefits to a broad group of lung cancer patients.”

“This has been a very productive industry-academic collaboration between Yale and Asuragen scientists” commented Matt Winkler CEO of Asuragen. “This work provides further evidence of the importance of miRNAs in the development of cancer and provides additional support for miRNA replacement therapy as an important component of effective cancer treatment regimens of the future.”

References for Cell Cycle Paper

Other authors on the paper were Aurora Esquela-Kerscher, Phong Trang and Joanne Weidhaas at Yale; Jason Wiggins, Lubna Patrawala, David Brown and Andreas Bader at Asuragen, Inc.; Angie Cheng and Lance Ford at Ambion, Inc. The work was funded by a grant from the State of Connecticut Department of Public Health and fellowships from the National Institutes of Health.

Citation: Cell Cycle (March 15, 2008).

LOS ALAMOS, New Mexico, March 10, 2008—A group of researchers has developed a novel way to view the world through the eyes of a common fly and partially decode the insect’s reactions to changes in the world around it. The research fundamentally alters earlier beliefs about how neural networks function and could provide the basis for intelligent computers that mimic biological processes.In an article published in the Public Library of Science Computational Biology Journal, Los Alamos physicist Ilya Nemenman joins Geoffrey Lewen, William Bialek and Rob de Ruyter van Steveninck of the Hun School of Princeton, Princeton University and Indiana University, respectively, in describing the research.

The team used tiny electrodes to tap into motion-sensitive neurons in the visual system of a common blowfly. Neurons are nerve cells that emit tiny electric spikes when stimulated. The electrodes detected pulses from the motion-sensitive neurons in the fly. The fly uses the neurons to estimate, and subsequently control, how it moves through the world.

The team harnessed the wired fly into an elaborate turntable-like mechanism that mimics the kind of acrobatic flight a fly might undergo while evading a predator or chasing another fly. The mechanism can spin extremely fast and change velocities quickly. A fly in the mechanism sees changes in the world around it and its motion-sensitive neurons react much in the same way as they would if the insect were actually flying.

Under complex flight scenarios, the fly’s neurons fired very quickly. The researchers looked at the firing patterns and mapped them with a binary code of ones and zeroes, much like computer instructions, or binary messages in digital phone communications.

The team found that the impulses were like a primitive, but very regular “language”—with the neuron firing at precise times depending on what the fly’s visual sensors were trying to tell the rest of the fly about the visual stimulus. When they examined this language, it spoke volumes about how the harnessed fly reacted to its world.

“In this system, the motion-sensitive neurons emit spikes very often and very precisely,” said Nemenman. “Historically, people have observed a lot more random spike intervals. This research is a departure from the traditional understanding in that we see that the precision of spike timing that carries information about the fly’s rotation is a factor of ten higher than even the most daring previous estimates.”

Similar-though-much-simpler experiments on different subjects, including flies, and going back to the seminal work of E. D. Adrian and Yngve Zotterman in 1926, seemed to show that sensory neurons would fire a certain number of impulses during a given period, but that the precise timing of the impulses was largely irrelevant. Nemenman and his team believe the timing of the spikes was not as crucial during those early experiments largely because the artificial stimulation was in some sense unnatural, bordering on the monotonous and predictable.

“Biological organisms have an interest in conserving energy,” Nemenman said. “Fly eyes account for about one-tenth of the fly’s energy consumption. The fly wants to be very efficient, but it costs energy and molecular resources to emit many precise spikes in the neurons.

“If you are presenting simple stimuli where little changes with time, then the most efficient way to encode them may be to generate few randomly positioned spikes, which would be sufficient to convey whatever small changes, if any, happened. Similarly, if the stimulus is unnaturally fast, the neurons may not be able to encode it well.

“However, if you put an organism in an environment with fast and naturally changing velocity profiles, the fly starts using all the bandwidth available to it,” Nemenman said. “The motion-sensitive neuron adjusts its coding strategy and it uses the precise positioning of the spikes to tell the rest of the fly exactly what is happening.”

In addition to the complex motions possible with the team’s apparatus, they conducted their experiment in a wooded setting similar to the fly’s natural environment, adding to the complexity and realism of the experiment.

Nemenman and his colleagues’ research is significant because it re-examines fundamental assumptions that became the basis of neuromimetic approaches to artificial intelligence, such as artificial neural networks. These assumptions have developed networks based on reacting to a number of impulses within a given time period rather than the precise timing of those impulses.

“This may be one of the main reasons why artificial neural networks do not perform anywhere comparable to a mammalian visual brain,” said Nemenman, who is a member of Los Alamos’ Computer, Computational and Statistical Sciences Division. “In fact, the National Science Foundation has recognized the importance of this distinction and has recently funded a project, led by Garrett Kenyon of the Laboratory’s Physics Division, to enable creation of large, next-generation neural networks.”

New understanding of neural function in the design of computers could assist in analyses of satellite images and facial-pattern recognition in high-security environments, and could help solve other national and global security problems.

Nemenman’s work on this project at Los Alamos is funded by the Laboratory Directed Research and Development Program, which strategically invests less than six percent of the institution’s annual budget in early exploration or growth of creative scientific concepts selected at the discretion of the Laboratory director.

Bacteria can be used to engineer genetic modifications, thereby providing scientists with a tool to combat many challenges in areas from food production to drug discovery. However, this sophisticated technology can also be used maliciously, raising the threat of engineered pathogens. New research published in the online open access journal Genome Biology shows that computational tools could become a vital resource for detecting rogue genetically engineered bacteria in environmental samples.Jonathan Allen, Shea Gardner and Tom Slezak of the Lawrence Livermore National Laboratory in California, US, designed new computational tools that identify a set of DNA markers that can distinguish between artificial vector sequences and natural DNA sequences. Natural plasmids and artificial vector sequences have much in common, but these new tools show the potential to achieve high sensitivity and specificity, even when detecting previously unsequenced vectors in microarray-based bioassays.

A new computational genomics tool was developed to compare all available sequenced artificial vectors with available natural sequences, including plasmids and chromosomes, from bacteria and viruses. The tool clusters the artificial vector sequences into different subgroups based on shared sequence; these shared sequences were then compared with the natural plasmid and chromosomal sequence information so as to find regions that are unique to the artificial vectors. Nearly all the artificial vector sequences had one or more unique regions. Short stretches of these unique regions are termed ‘candidate DNA signatures’ and can be used as probes for detecting an artificial vector sequence in the presence of natural sequences using a microarray. Further tests showed that subgroups of candidate DNA signatures are far more likely to match unseen artificial than natural sequences.

The authors say that the next step is to see whether a bioassay design using DNA signatures on microarrays can spot genetically modified DNA in a sample containing a mixture of natural and modified bacteria. The scientific community will need to cooperate with computational experts to sequence and track available vector sequences if DNA signatures are to be used successfully to support detection and deterrence against malicious genetic engineering applications. Scientists would be able to maintain an expanding database of DNA signatures to track all sequenced vectors.

“As with any attempt to counter malicious use of technology, detecting genetic engineering in microbes will be an immense challenge that requires many different tools and continual effort,” says Allen.

References

1. DNA signatures for detecting genetic engineering in bacteria
Jonathan E Allen, Shea N Gardner and Tom R Slezak
Genome Biology (in press)

Article available here:
http://genomebiology.com/imedia/1534720787156665_article.pdf?random=277103

A group of researchers have developed a computer algorithm that can imitate the bat’s ability to classify plants using echolocation. The study, published March 21st in the open-access journal PLoS Computational Biology, represents a collaboration between machine learning scientists and biologists studying bat orientation.To detect plants, bats emit ultrasonic pulses and decipher the various echoes that return. Bats use plants daily as food sources and landmarks for navigation between foraging sites. Plant echoes are highly complex signals due to numerous reflections from leaves and branches. Classifying plants or other intricate objects, therefore, has been considered a troublesome task for bats and the scientific community was far from understanding how they do it.

Now, a research group in Tübingen, Germany, including University of Tübingen researchers Yossi Yovel, Peter Stilz and Hans Ulrich-Schnitzler, and Matthias Franz from the Max Planck Institute of Biological Cybernetics, has demonstrated that this process of plant classification is not as difficult as previously thought.

The group used a sonar system to emit bat-like, frequency-modulated ultrasonic pulses. The researchers recorded thousands of echoes from live plants of five species. An algorithm that uses the time-frequency information of these echoes was able to classify plants with high accuracy. This new algorithm also provides hints toward which echo characteristics might be best understood by the bats.

According to the group, these results enable us to improve our understanding of this fascinating ability of how bats classify plants, but do so without entering the bat’s brain.

http://www.ploscompbiol.org/doi/pcbi.1000032 (link will go live on Friday, March 21)

CITATION: Yovel Y, Franz MO, Stilz P, Schnitzler H-U (2008) Plant Classification from Bat-Like Echolocation Signals. PLoS Comput Biol 4(3): e1000032. doi:10.1371/journal.pcbi.1000032

DURHAM, N.C. – Investigators at the Duke Institute for Genome Sciences and Policy have revealed the hidden properties of an on-off switch that governs cell growth.The Duke team proved that if the switch is on, then a cell will divide, even if it’s damaged or the signal to grow disappears. Showing how the switch works may provide clues to novel drug targets for cancer and other diseases in which cell growth goes awry.

The switch is part of a critical pathway that controls cell division, the process by which the body makes new cells. Before a cell starts to divide, it goes through a checklist to make sure everything is in order, much like preparing for a long trip. If a cell senses something is wrong early on, it can halt the process. But once a cell passes a milestone called the restriction point, there’s no turning back, no matter the consequences. The switch controls this milestone and is key to cell growth.

The results will appear in the April issue of the journal Nature Cell Biology. The study was funded by the National Institutes of Health, the National Science Foundation and a David and Lucile Packard Fellowship.

The switch is part of the Rb-E2F signaling pathway. Rb, or retinoblastoma, is a key tumor suppressor gene, and E2F is a transcription factor that governs the expression of all the genes important for cells to grow.

“The wiring diagram is fundamentally the same. It’s very likely that different organisms have evolved a very conserved design principle to regulate their growth,” said Guang Yao, Ph.D., lead study author and a postdoctoral fellow in Duke’s department of molecular genetics and microbiology.

The cellular pathway that includes the switch is found in all multi-cellular life, from plants to people. A cell decides to trigger the pathway when it receives an external chemical signal to grow.

During the project, the researchers discovered the switch has an unexpected property: it is bistable. Once turned on by an external signal, the switch can maintain its on state, even if the signal disappears.

It was an engineer, Lingchong You, Ph.D., who recognized that the switch might represent a bistable condition. You, an assistant professor of biomedical engineering in Duke’s Pratt School of Engineering and an Institute for Genome Sciences & Policy (IGSP) investigator, works next door to Yao and his postdoctoral advisor Joseph Nevins, Ph.D., a professor of molecular genetics at the IGSP.

During conversations with Nevins and Yao about the restriction point phenomenon, You realized that the process could be described as a bistable switch.

The collaboration continued as the scientists broke down the pathway into individual chemical reactions that could be described by mathematical equations. Graduate student Tae Jun Lee worked with Yao to develop and analyze a mathematical model that predicted the switch could be bistable and identified the critical decision maker at the restriction point. Yao verified the results in laboratory experiments on single cells.

Nevins, who has studied the Rb-E2F pathway for 20 years, sees an opportunity to extend this approach to other critical aspects of cell behavior, such as the decisions involved in cell death.

“This pathway, and this decision whether it is time to proliferate, is very tightly coupled to decisions of cell fate,” Nevins said. “There’s a decision as to whether the proliferation process is normal, and if the answer is not, then the result is that the cell dies. We don’t know critical dynamics of that process.”

HOUSTON — A protein known as REST blocks the expression of a microRNA that prevents embryonic stem cells from reproducing themselves and causes them to differentiate into specific cell types, scientists at The University of Texas M. D. Anderson Cancer Center report in the journal Nature.Researchers show RE1-silencing transcription factor (REST) plays a dual role in embryonic stem cells, said senior author Sadhan Majumder, Ph.D., professor in M. D. Anderson’s Department of Cancer Genetics. “It maintains self-renewal, or the cell’s ability to make more and more cells of its own type, and it maintains pluripotency, meaning that the cells have the potential to become any type of cell in the body.”

The paper posted online March 23 in advance of publication grew from M. D. Anderson research on the protein’s role in medulloblastoma – an exceptionally aggressive pediatric brain cancer.

Embryonic stem cells are essentially blank slates. They have the unique ability to develop from identical, unspecialized cells and then differentiate into distinct types of cells with special functions. In the laboratory, scientists have been able to induce embryonic stem cells to develop into heart muscle cells or insulin-producing cells of the pancreas. The hope is that embryonic stem cells might one day be used to restore or replace failing cells in the human body and perhaps treat a wide range of diseases.

“Embryonic stem cells have a very high potential in medicine,” Majumder said. “The critical thing is to learn the mechanisms that could be used to generate a lot of self-renewing embryonic stem cells and be able to differentiate them into various cell types.” REST could play a key role in maintaining a steady supply of these cells and in preserving their differentiation capability.

Suppressing MicroRNA-21

In studies using mouse embryonic stem cells, the researchers found that REST disarms a specific microRNA called microRNA-21 or miR-21. MicroRNAs are tiny pieces of RNA that control gene expression by binding to the gene’s messenger RNA.

The team found that MiR-21 suppresses embryonic stem cell self-renewal and is associated with a corresponding loss of expression of critical self-renewal regulators, such as Oct4, Nanog, Sox2 and c-Myc. REST counters this by suppressing miR-21 to preserve the cells’ self-renewal and pluripotency.

The researchers discovered the roles of REST and miR-21 in a series of experiments using cultured mouse embryonic stem cells in either a self-renewal state or a differentiating state. They found that REST expression was significantly higher in the self-renewal state. Withdrawing REST reduced the stem cells’ ability to reproduce themselves and started differentiation — even when the cells were grown under conditions conducive to self-renewal. Adding REST to differentiating cells maintained their self-renewal.

These experiments also revealed that REST is bound to the gene chromatin of a set of microRNAs with the potential to target self-renewal genes. REST controls transcription of 11 microRNAs.

REST Implicated in Pediatric Brain Cancer

Previous laboratory research suggests that the qualities that make REST beneficial in stem cell production and pluripotency may contribute to the development of medulloblastoma, an aggressive type of children’s brain tumor. Medulloblastomas are believed to develop from undifferentiated neural stem cells in the external granule layer of the cerebellum.

In earlier research, Majumder’s group at M. D. Anderson discovered that about half of these tumors overexpress REST, which is not found in most neural cells. “We found that REST is a critical factor in this group of children’s brain tumors,” Majumder said, “and that its major function is to keep a group of specific brain stem cells, or progenitor cells, in a state of stemness.”

The researchers hypothesize that by maintaining the neural stem cells’ ‘stemness,’ REST prevents their differentiation into normal and distinct types of cells, leading instead to tumor formation. The M. D. Anderson scientists are now exploring whether microRNAs might also play a role in medulloblastomas.

Understanding REST function has applications in both medulloblastoma and embryonic stem cell biology. “Just as blocking REST function has therapeutic potential in medulloblastoma, blocking REST function to allow for differentiation of embryonic stem cells is a potentially critical step in regenerative medicine,” Majumder said.

Viruses and bacterial viruses (known as phages) are among the most abundant life forms on the planet. Two papers published recently in Nature, March 2 and 12, 2008, analyse the geographical distribution of viral communities in modern organosedimentary structures (sedimentary features, built by the interaction of organisms and their environment) known as microbialites, the living analogues of the oldest fossils on Earth, and come up with some surprising nuggets of information.Microbialites first appeared in the geological record, 3.5 billion years ago, and for more than 2 billion years they are the main evidence of life on Earth. A team of scientists from US and Singapore used a comparative metagenomics approach to show that phages associated with such structures are very different not only from each other but also from those found in any other ecosystem so far. The team’s findings indicate that modern microbialites are endemic remnants of ancient ecosystems.

Dr Ruan Yijun, Senior Group Leader at the Genome Institute of Singapore (GIS), said, “Using DNA sequencing technology, we were able to identify unknown viruses in various environments relevant to human health. This collaboration is the first ever large-scale effort to analyse biodiversity and biogeography of viruses in the environments around humans.”

“We have been interested in this kind of analysis since the SARS (severe acute respiratory syndrome) outbreak in 2002,” added Dr Ruan. “In pursuit of this interest, we established a virus discovery programme at GIS, resulting in the discovery of abundant viruses in the human gut (PLoS Biology, 2006) and different variants of dengue viruses. Now, with more viral metagenomic data accumulated, we are able to summarise the biodiversity and biogeography on a global scale.”

Microbialites are organosedimentary structures accreted by sediment trapping, binding and in situ precipitation due to the growth and metabolic activities of microorganisms.

Stromatolites and thrombolites are morphological types of microbialites classified by their internal mesostructure: layered and clotted, respectively.

###

Notes to the Editor:

Research publication:

The research findings described in the press release can be found in the March 2, 2008 issue of Nature under the title “Biodiversity and biogeography of phages in modern stromatolites and thrombolites”; and the March 12, 2008 issue of Nature under the title “Functional metagenomic profiling of nine biomes”.

Authors for March 2 paper:

Christelle Desnues1, Beltran Rodriguez-Brito1,2, Steve Rayhawk1,2, Scott Kelley1,3, Tuong Tran1, Matthew Haynes1, Hong Liu1, Mike Furlan1, Linda Wegley1, Betty Chau1, Yijun Ruan4, Dana Hall1, Florent E. Angly1, Robert A. Edwards1,2,3,5, Linlin Li1, Rebecca Vega Thurber1, R. Pamela Reid6, Janet Siefert7, Valeria Souza8, David L. Valentine9, Brandon K. Swan9, Mya Breitbart10 & Forest Rohwer1,3

1. Department of Biology,
2. Computational Sciences Research Center,
3. Center for Microbial Sciences, San Diego State University, San Diego, California 92182, USA.
4. Genome Institute of Singapore, Singapore 138672, Singapore.
5. Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
6. Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida 33149, USA.
7. Department of Statistics, Rice University, Houston, Texas 77251, USA.
8. Departamento de Ecologı´a Evolutiva, Instituto de Ecologı´a, Universidad Nacional Auto´noma de Me´xico AP 70-275 Coyoaca´n, 04510 Mexico D.F., Mexico.
9. Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106, USA.
10. College of Marine Science, University of South Florida, St Petersburg, Florida 33701, USA.

Authors for March 12 paper:

Elizabeth A. Dinsdale1,5*, Robert A. Edwards1,2,3,6*, Dana Hall1, Florent Angly1,4, Mya Breitbart7, Jennifer M. Brulc8, Mike Furlan1, Christelle Desnues1{, Matthew Haynes1, Linlin Li1, Lauren McDaniel7, Mary Ann Moran10, Karen E. Nelson11, Christina Nilsson12, Robert Olson6, John Paul7, Beltran Rodriguez Brito1,4, Yijun Ruan12, Brandon K. Swan13, Rick Stevens6, David L. Valentine13, Rebecca Vega Thurber1, Linda Wegley1, Bryan A. White8,9 & Forest Rohwer1,2

1 Department of Biology,
2 Center for Microbial Sciences,
3 Department of Computer Sciences, and
4 Computational Science Research Centre, San Diego State University, San Diego, California 92182, USA.
5 School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia.
6 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
7 University of South Florida, College of Marine Science, 140 7th Avenue South, St Petersburg, Florida 33701, USA.
8 Department of Animal Sciences, and
9 The Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA.
10 Department of Marine Sciences, University of Georgia, Athens, 30602 Georgia, USA.
11 The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
12 Genome Institute of Singapore, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore.
13 Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106, USA.
{ Present address: Unite des Rickettsies, CNRS-UMR 6020, Faculte de medecine, 13385 Marseille, France.

About the Genome Institute of Singapore
www.gis.a-star.edu.sg

The Genome Institute of Singapore (GIS) is a member of the Agency for Science, Technology and Research (A*STAR). It is a national initiative with a global vision that seeks to use genomic sciences to improve public health and public prosperity. Established in 2001 as a centre for genomic discovery, the GIS will pursue the integration of technology, genetics and biology towards the goal of individualized medicine. The key research areas at the GIS include Systems Biology, Stem Cell & Developmental Biology, Cancer Biology & Pharmacology, Human Genetics, Infectious Diseases, Genomic Technologies, and Computational & Mathematical Biology. The genomics infrastructure at the GIS is utilized to train new scientific talent, to function as a bridge for academic and industrial research, and to explore scientific questions of high impact.

About the Agency for Science, Technology and Research
www.a-star.edu.sg

The Agency for Science, Technology and Research, or A*STAR, is Singapore’s lead agency for fostering world-class scientific research and talent for a vibrant knowledge-based Singapore. A*STAR actively nurtures public sector research and development in Biomedical Sciences, Physical Sciences and Engineering, with a particular focus on fields essential to Singapore’s manufacturing industry and new growth industries. It oversees 14 research institutes and supports extramural research with the universities, hospital research centres and other local and international partners. At the heart of this knowledge intensive work is human capital. Top local and international scientific talent drive knowledge creation at A*STAR research institutes. The Agency also sends scholars for undergraduate, graduate and post-doctoral training in the best universities, a reflection of the high priority A*STAR places on nurturing the next generation of scientific talent.

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