Preventing Cancer Development Inside the Cell Cycle

Researchers from the NYU Cancer Institute, an NCI-designated cancer center at NYU Langone Medical Center, have identified a cell cycle-regulated mechanism behind the transformation of normal cells into cancerous cells. The study shows the significant role that protein networks can play in a cell leading to the development of cancer. The study results, published in the October 21 issue of the journal Molecular Cell, suggest that inhibition of the CK1 enzyme may be a new therapeutic target for the treatment of cancer cells formed as a result of a malfunction in the cell's mTOR signaling pathway.

In the study, NYU Cancer Institute researchers examined certain multi-protein complexes and protein regulators in cancer cells. Researchers identified a major role for the multi-protein complex called SCF^βTrCP. It assists in the removal from cancer cells the recently discovered protein DEPTOR, an inhibitor of the mTOR pathway. SCF (Skp1, Cullin1, F-box protein) ubiquitin ligase complexes are responsible for the removal of unnecessary proteins from a cell. This degradation of proteins by the cell's ubiquitin system controls cell growth and prevents malignant cell transformation. Researchers show that inhibiting the ability of SCF^βTrCPto degrade DEPTOR in cells can result in blocking the proliferation of cancer cells. In addition, researchers discovered that the activity of CK1 (Casein Kinase 1), a protein that regulates signaling pathways in most cells, is needed for SCF^βTrCP to successfully promote the degradation of DEPTOR.

"Low levels of DEPTOR and high levels of mTOR activity are found in many cancers, including cancers of the breast, prostate, and lung," said senior study author Michele Pagano, MD, the May Ellen and Gerald Jay Ritter Professor of Oncology and Professor of Pathology at NYU Langone Medical Center and a Howard Hughes Medical Institute Investigator. "It is critical for researchers to better understand how the protein DEPTOR is regulated.Our study shows it would be advantageous to increase the levels of DEPTOR in many types of cancer cells to inhibit mTOR and prevent cell proliferation."

The mTOR pathway (mammalian Target Of Rapamycin) regulates the growth, proliferation, and survival of a cell, and its proper regulation is essential to prevent the formation of cancer cells. DEPTOR interrupts the mTOR pathway by binding to mTOR protein complexes and blocking their enzymatic activities, restraining cell growth. This helps support the proliferation and survival of cancer cells.

Study experiments showed that a reduction of SCF^βTrCP and CK1 proteins in cells resulted in accumulation of DEPTOR. Also, DEPTOR was destroyed in cells only when SCF^βTrCP and CK1 were both present. Thus, inhibition of SCF^βTrCP or CK1 represents a novel and promising way to inhibit the mTOR pathway. A pharmacologic inhibitor of CK1 was tested by researchers and shown to successfully stabilize DEPTOR in cells, while other pharmacological agents had no effect.

"Our study findings demonstrate that DEPTOR is regulated by the SCF^βTrCPprotein complex in cells reentering the cell cycle, and deregulation of this event could contribute to the aberrant activation of the mTOR pathway in cancer," said lead author Shanshan Duan, PhD, a post-doctoral fellow in the Department of Pathology at NYU School of Medicine in Dr. Pagano's Laboratory. "This study suggests a novel approach to stop the deregulation of the mTOR pathway in cancer cells with promising small molecule inhibitors of CK1.This study is another step forward in the translation of laboratory findings into more effective approaches to cancer prevention and treatment."

Journal References:

1. Shanshan Duan, Jeffrey R. Skaar, Shafi Kuchay, Alfredo Toschi, Naama Kanarek, Yinon Ben-Neriah, Michele Pagano. mTOR Generates an Auto-Amplification Loop by Triggering the βTrCP- and CK1α-Dependent Degradation of DEPTOR. Molecular Cell, 2011; 44 (2): 317-324 DOI: 10.1016/j.molcel.2011.09.005
2. Shanshan Duan, Jeffrey R. Skaar, Shafi Kuchay, Alfredo Toschi, Naama Kanarek, Yinon Ben-Neriah, Michele Pagano. mTOR Generates an Auto-Amplification Loop by Triggering the βTrCP- and CK1α-Dependent Degradation of DEPTOR. Molecular Cell, 21 October 2011; 44(2) pp. 317 - 324 DOI: 10.1016/j.molcel.2011.09.005

Courtesy: ScienceDaily

Antiviral Drugs May Slow Alzheimer's Progression

Antiviral drugs used to target the herpes virus could be effective at slowing the progression of Alzheimer's disease (AD), a new study shows.

The University of Manchester scientists have previously shown that the herpes simplex virus type 1 (HSV1) is a risk factor for Alzheimer's when it is present in the brains of people who have a specific genetic risk to the disease.

AD is an incurable neurodegenerative condition affecting about 18 million people worldwide. The causes of the disease or of the abnormal protein structures seen in AD brains -- amyloid plaques and neurofibrillary tangles -- are completely unknown.

The Manchester team has established that the herpes virus causes accumulation of two key AD proteins -- β-amyloid (Aβ) and abnormally phosphorylated tau (P-tau) -- known to be the main components of plaques and tangles respectively. Both proteins are thought by many scientists to be involved in the development of the disease.

"We have found that the viral DNA in AD brains is very specifically located within amyloid plaques," said Professor Ruth Itzhaki, who led the team in the University's Faculty of Life Sciences. "This, together with the production of amyloid that the virus induces, suggests that HSV1 is a cause of toxic amyloid products and of plaques.

"Our results suggest that HSV1, together with the host genetic factor, is a major risk for AD, and that antiviral agents might be used for treating patients to slow disease progression."

Currently available antiviral agents act by targeting replication of HSV1 DNA, and so the researchers considered that they might be successful in treating AD only if the accumulation of β-amyloid and P-tau accumulation caused by the virus occurs at or after the stage at which viral DNA replication occurs.

"If these proteins are produced independently of HSV1 replication, antivirals might not be effective," said Professor Itzhaki. "We investigated this and found that treatment of HSV1-infected cells with acyclovir, the most commonly used antiviral agent, and also with two other antivirals, did indeed decrease the accumulation of β-amyloid and P-tau, as well as decreasing HSV1 replication as we would expect.

"This is the first study investigating antiviral effects on AD-like changes and we conclude that since antiviral agents reduce greatly β-amyloid and P-tau levels in HSV1-infected cells, they would be suitable for treating Alzheimer's disease. The great advantage over current AD therapies is that acyclovir would target only the virus, not the host cell or normal uninfected cells. Further, these agents are very safe and are relatively inexpensive.

"Also, by targeting a cause of Alzheimer's disease, other viral damage, besides β-amyloid and P-tau, which might be involved in the disease's pathogenesis, would also be inhibited.

"The next stage of our research -- subject to funding -- will focus on finding the most suitable antiviral agent -- or combination of two agents that operate via different mechanisms -- for use as treatment. We then need to investigate the way in which the virus and the genetic risk factor interact to cause the disease, as that might lead to further novel treatments.

"Eventually, we hope to begin clinical trials in humans but this is still some way off yet and again will require new funding."

The study, carried out with Dr Matthew Wozniak and other colleagues in the Faculty of Life Sciences, is published in the Public Library of Science (PLoS) One journal.

Journal Reference:

1. Matthew A. Wozniak, Alison L. Frost, Chris M. Preston, Ruth F. Itzhaki. Antivirals Reduce the Formation of Key Alzheimer's Disease Molecules in Cell Cultures Acutely Infected with Herpes Simplex Virus Type 1. PLoS ONE, 2011; 6 (10): e25152 DOI: 10.1371/journal.pone.0025152

Courtesy: ScienceDaily

Newly Discovered Reservoir of Antibiotic Resistance Genes

Waters polluted by the ordure of pigs, poultry, or cattle represent a reservoir of antibiotic resistance genes, both known and potentially novel. These resistance genes can be spread among different bacterial species by bacteriophage, bacteria-infecting viruses, according to a paper in the October Antimicrobial Agents and Chemotherapy.

"We found great quantities of bacteriophages carrying different antibiotic resistance genes in waters with fecal pollution from pigs, cattle, and poultry," says Maite Muniesa of the University of Barcelona, Spain, an author on the study. "We demonstrated that the genes carried by the phages were able to generate resistance to a given antibiotic when introduced into other bacteria in laboratory conditions," says Muniesa.

Although we often think of antibiotic resistance genes as evolving into existence in response to the antibiotics that doctors use to fight human disease and that agribusiness uses to fatten farm animals, microbes had undoubtedly been using both antibiotics and resistance genes to compete with each other for millions of years before antibiotics revolutionized human medicine and resistance genes threatened their efficacy to the point where the World Health Organization considers them to be one of the biggest risks to human health.

Thus, the Spanish researchers suspect, based on their study, that these resistance gene reservoirs are the product of microbial competition, rather than pressure from human use of antibiotics. They note that the pasture-fed cattle in their study are not fed antibiotics, and they suggest that even if antibiotic feed additives were banned, new resistance genes might emerge while old ones spread from these reservoirs into bacteria that infect humans.

And if resistance genes are being mobilized from these reservoirs, it becomes important to understand how the resistance genes are transmitted from phage to new bacterial species, in order to develop strategies that could hinder this transmission, limiting the emergence of new resistance genes, says Muniesa.

Journal Reference:

1. M. Colomer-Lluch, L. Imamovic, J. Jofre, M. Muniesa. Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry. Antimicrobial Agents and Chemotherapy, 2011; 55 (10): 4908 DOI: 10.1128/AAC.00535-11

Courtesy: ScienceDaily

Hidden Genetic Influence On Cancer Discovered

In findings with major implications for the genetics of cancer and human health, researchers at Beth Israel Deaconess Medical Center (BIDMC) and two other science teams in New York City and Rome have uncovered evidence of powerful new genetic networks and showed how it may work to drive cancer and normal development.

Four papers published online Oct. 14 in the journal Cell describe aspects of what may be a fundamentally new dimension of genetic activity that involves a vast posse of RNA molecules interacting and manipulating the molecular endgame behind the scenes. Each paper used a different approach, strengthening the basic discovery of the new RNA network.

In the half-century old central dogma of molecular biology, DNA issues its genetic blueprint to messenger RNA, which relays the orders to the protein-making machinery of the cell. The new studies suggest a significant new role for RNA on top of its traditional middle-management job: The RNA of one gene can control and be controlled by dozens or hundreds of RNAs of other genes.

In the case of a major tumor suppressor gene, PTEN, a shift in the associated RNA network appears to be as malevolent as a mutation in the gene itself in human prostate and colon cancer cells, in glioblastoma cells, and in a mouse model of melanoma, according to three of the papers.

The findings may enlarge the framework for investigating how tumors form and progress, who is at risk for cancer, and how to find and disable the essential misbehaving molecules that drive the growth and spread of cancer.

"For instance, we now know that the PTEN tumor suppressor gene is talking to a vast unrecognized RNA network," said Pier Paolo Pandolfi MD PhD, director of the Cancer Genetics Program at BIDMC and George C. Reisman Professor of Medicine at Harvard Medical School, and the senior author of two of the papers. "The RNAs talk through a new language. If this language is broken and the RNA network is perturbed, PTEN goes down, and this has devastating consequences. But it's incredibly exciting for therapeutic possibilities. You may be able to rewire the crosstalk between the RNAs for cancer prevention and therapy."

Scientists typically use genetic studies to probe how changes in the DNA code influence the action of the proteins. Targeted therapies have arisen from efforts to counteract the effect of problematic proteins, yet most of the genetic determinants of cancer remain a vexing puzzle. The newly discovered RNA network could explain much of the elusive genetic variation underlying cancer and other diseases, say authors of the papers.

The new RNA regulatory network also appears to extend into the massive non-protein-coding region of the human genome and plays an important role in normal muscle development, suggests another related paper in Cell. Because humans share so many protein-coding genes with other organisms, including worms and yeast, this large portion that is transcribed into non-coding RNA makes the human genome distinctive. Much of the function of that non-coding RNA has been a mystery.

"Almost all of the scientific analysis of cancer genes focuses on the protein-coding genes," Pandolfi said, referring to the two percent of the human genome where instructions are passed from DNA to RNA to proteins. "We know that nearly half of the genome is transcribed into RNA that doesn't code for protein. Through this new 'language' of RNA, we can functionalize this space."

How it works

The newly discovered network of RNA molecules converse through tiny targeted molecules called microRNAs, Pandolfi and his colleagues have found. RNAs share a vocabulary composed of specific sequences along their strands called microRNA response elements (MREs). RNAs compete for certain matching microRNAs. Once attached, microRNAs disable their host RNA molecules. It works through simple math: An increase in RNA can sponge up more microRNA, allowing other RNA to go about their business unhindered.

Scientists have known for a decade that microRNA can block RNA and prevent it from being translated into proteins. Some research has advanced to harnessing specific small microRNA molecules as experimental therapeutic tools to block individual protein-coding genes. What's new in the Cell papers is the idea of reverse logic -- that a large RNA network uses microRNA as a regulatory language.

Tantalizing hints of this newfound regulatory network have shown up in recent studies from several labs. Last year, Pandolfi's group reported that both PTEN and its nemesis, the common cancer-promoting gene KRAS, have doppelgangers known as pseudogenes in the non-coding regions of the genome, which act as decoys for targeted microRNA, greatly influencing the activity of the two cancer genes.

This August, Pandolfi and his co-authors named this RNA language and network activity "competing endogenous RNA" (ceRNA, pronounced SIR-na) in a Cell essay. The paper synthesized the emerging experimental evidence in a new theory. They proposed that ceRNA activity greatly expanded the functional genetic information in the human genome and played important roles in diseases, including cancer.

The ceRNA hypothesis adds a major new layer to the highly regulated basic players defined by the central dogma of molecular biology -- DNA, RNA and proteins. Other more established regulatory networks that keep cells healthy -- and break down in disease -- include small molecules added to proteins, such as the recycling label called ubiquitin. Another layer called epigenetics acts on the DNA and its packaging to lock or unlock certain genes.

The findings in the papers

Two of the Cell papers use a combination of bioinformatics and experimental evidence to connect the PTEN tumor suppressor gene to a network of several hundred RNA molecules in close communication.

One of the new papers from the Pandolfi lab linked about 150 new genes to the tumor suppressor PTEN in human prostate and colon cancer cell lines. Working with a collaborator at Jefferson Medical College in Philadelphia, postdoctoral fellow Yvonne Tay and her co-authors scanned the RNA transcripts of protein-coding genes based on their MRE sequences and then tested a few of the results. "Surprisingly, PTEN can be regulated by a lot of other genes through the ceRNA network," Tay said.

In an independent paper, a team in the lab of Andrea Califano at Columbia University in New York evaluated glioblastoma RNA and microRNA expression data from The Cancer Genome Atlas, a public database. They found a network in which more than 500 genes regulate PTEN. Of these, 13 are frequently deleted in glioblastoma and seem to work together through the microRNA language to squelch the tumor suppressor activity as if the tumors had mutations or deletions of PTEN itself.

"All these papers address different aspects of this compelling story and reinforce each other," said Califano, who also found RNA networks that appeared to communicate by other means. "PTEN is just an example. In each cell, different cliques of genes are connected by this microRNA-mediated network, including all the established oncogenes and tumor suppressors. This layer explains a significant amount of genetic variability in cancer. It allows genes that have nothing to do with the typical oncogene or tumor suppressor to gang up and regulate it. The discovery of this network allows us to discover genes never before associated with a tumor type or disease."

In a second paper from the Pandolfi group, mutations in the PTEN RNA network speeded up the growth of cancer in a mouse model of melanoma. Postdoctoral fellow Florian Karreth and his co-authors discovered possible new PTEN ceRNAs in a mutagenesis screen of a mouse model of melanoma. With the help of a bioinformatics team from the University of Turin, they did an in-depth analysis of one ceRNA (ZEB2) that is reduced in human cancer and verified that its reduction accelerated cancer progression in the mice. Interestingly, while the ZEB2 ceRNA opposes melanoma by sponging the microRNAs that would otherwise repress PTEN's tumor suppression activity, the ZEB2 protein is known to promote other cancers. "It is astonishing that RNA and protein molecules encoded by the same gene can take part in opposing biological processes," Karreth said.

The final study extends functional evidence of the new RNA network phenomenon to the normal differentiation of human muscle cells and to the large realm of human non-coding RNAs. Irene Bozzoni's group at the Sapienza University of Rome found that a long non-protein coding RNA works similarly as a decoy for microRNAs in normal muscle differentiation in mice and humans. In Duchenne muscular dystrophy, the decoy RNA is missing at a crucial time, preventing muscle cells from maturing.

"This explains in part why Duchenne cells have trouble, and it gives us another circuitry to attack in order to cure the disease," said Bozzoni, who heard about Pandolfi's ceRNA hypothesis at a meeting last year. "We have been working on noncoding RNA and microRNA for quite a long time. This cross-talk of RNAs through microRNAs is a revolutionary idea."

Journal References:

1. Yvonne Tay, Lev Kats, Leonardo Salmena, Dror Weiss, Shen Mynn Tan, Ugo Ala, Florian Karreth, Laura Poliseno, Paolo Provero, Ferdinando Di Cunto, Judy Lieberman, Isidore Rigoutsos, Pier Paolo Pandolfi. Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs. Cell, 2011; 147 (2): 344-357 DOI: 10.1016/j.cell.2011.09.029
2. Florian A. Karreth, Yvonne Tay, Daniele Perna, Ugo Ala, Shen Mynn Tan, Alistair G. Rust, Gina DeNicola, Kaitlyn A. Webster, Dror Weiss, Pedro A. Perez-Mancera, Michael Krauthammer, Ruth Halaban, Paolo Provero, David J. Adams, David A. Tuveson, Pier Paolo Pandolfi. In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma. Cell, 2011; 147 (2): 382-395 DOI: 10.1016/j.cell.2011.09.032
3. Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, Jose Silva, Andrea Califano. An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma. Cell, 2011; 147 (2): 370-381 DOI: 10.1016/j.cell.2011.09.041
4. Marcella Cesana, Davide Cacchiarelli, Ivano Legnini, Tiziana Santini, Olga Sthandier, Mauro Chinappi, Anna Tramontano, Irene Bozzoni. A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA. Cell, 2011; 147 (2): 358-369 DOI: 10.1016/j.cell.2011.09.028

Courtesy: ScienceDaily

Understanding the Beginnings of Embryonic Stem Cells Helps Predict the Future

Scientists have shown that laboratory-grown cells express a protein called Blimp1, which represses differentiation to somatic or regular tissue cells during germ cell development. Studies of these cells show that they also express other genes associated with early germ cell specification.

Ordinarily, embryonic stem cells exist only a day or two as they begin the formation of the embryo itself. Then they are gone.

In the laboratory dish, however, they act more like perpetual stem cells -- renewing themselves and exhibiting the ability to form cells of almost any type, a status called totipotency.

Dr. Thomas Zwaka, associate professor in the Stem Cell and Regenerative Medicine Center at Baylor College of Medicine, and his colleagues here and abroad showed that laboratory-grown cells express a protein called Blimp1, which represses differentiation to somatic or regular tissue cells during germ cell development. Studies of these cells show that they also express other genes associated with early germ cell specification.

A report on their work published online October 13 in the journal Current Biology. It will appear in the October 25 print edition of the journal.

"What are embryonic stem cells?" said Zwaka, who is also part of the Center for Cell and Gene Therapy at BCM, Texas Children's Hospital and The Methodist Hospital. "It is quite a surprise that we have them. In the embryo, there is a mass of cells that eventually form the embryo, but they do not persist. They do not have a program built in that allows them to persist."

To study this, he examined mice. If you put the mass of cells in a Petri dish in the laboratory, they act as thought they are stem cells with the ability for self renewal and totipotency -- the ability to become almost any kind of cell.

Understanding what happens early in development of embryonic stem cells in the laboratory might help make the process of growing them and another, new kind of stem cell called induced pluripotent stem cells -- cells with the potential of becoming many different kinds of tissues that are derived from somatic or adult cells.

"These induced pluripotent stem cells are poorly understood," said Zwaka. "If we know what is happening when we derive embryonic stem cells in the laboratory, it will inform us when we make induced pluripotent stem cells. The end product is similar."

The process of making the induced pluripotent stem cells is noisy and random, he said.

"Every time, the clones look different and emerge at different time points," said Zwaka. By contrast, embryonic development is like clockwork, with events occurring at the same point with each embryo. However, development of embryonic stem cells in the laboratory becomes more disorganized as time goes on.

In the laboratory dish, the mouse embryo continues to develop at a fairly organized rate for two or three days, but when the single cells are separated and grown singly, the embryonic stem cells begin to emerge. Only a tiny subset -- roughly 1 percent -- of the cells become an embryonic stem cell in the laboratory."

"We found that these cells (from the embryonic stem cells come) resemble in almost every feature an early germ cell (primordial germ cell)," he said. (Primordial germ cells are the source of gametes -- eggs and sperm.)

"It seems that these seeming germ cells are the cells that make the embryonic stem cells in culture," he said.

"Germ cells in the embryo are unique and pluripotent (able to become many different kinds of cells) and have a very sophisticated program in them that protects the from becoming somatic cells (specific tissue cells)," he said. "They retain their primitive state." Blimp1 is a master regulator of germ cells.

In the future, he said, he hopes that investigators in both fields can collaborate and learn from one another.

Others who took part in this research include Li-Fang Chua of BCM, M. Azim Surani of the Wellcome Trust Cancer Research UK Gurdon Institute at the University of Cambridge, and Rudolf Jaenisch of Whitehead Institute for BiomedicaI Research at the Massachusetts Institute of Technology in Cambridge.

Funding for this work came from the Huffington Foundation and the National Institutes of Health.

For more information on basic science research at Baylor College of Medicine, please go to From the Lab at Baylor College of Medicine.

Journal Reference:

1. Li-Fang Chu, M. Azim Surani, Rudolf Jaenisch, Thomas P. Zwaka. Blimp1 Expression Predicts Embryonic Stem Cell Development In Vitro. Current Biology, 13 October 2011 DOI: 10.1016/j.cub.2011.09.010

Courtesy: ScienceDaily

Uncharted Territory: Scientists Sequence the First Carbohydrate Biopolymer

DNA and protein sequencing have forever transformed science, medicine, and society. Understanding the structure of these complex biomolecules has revolutionized drug development, medical diagnostics, forensic science, and our understanding of evolution and development. But, one major molecule in the biological triumvirate has remained largely uncharted: carbohydrate biopolymers.

Today, for the first time ever, a team of researchers led by Robert Linhardt of Rensselaer Polytechnic Institute has announced in the October 9 Advanced Online Publication edition of the journal Nature Chemical Biology the sequence of a complete complex carbohydrate biopolymer. The surprising discovery provides the scientific and medical communities with an important and fundamental new view of these vital biomolecules, which play a role in everything from cell structure and development to disease pathology and blood clotting.

The paper is titled "The proteoglycan bikunin has a defined sequence."

"Carbohydrate biopolymers, known as glycosaminoglycans, appear to be really important in how cells interact in higher organisms and could explain evolutionary differences and how development is driven. We also know that carbohydrate chains respond to disease, injury, and changes in the environment," said Linhardt, who is the Ann and John H. Broadbent Jr. '59 Senior Constellation Professor of Biocatalysis and Metabolic Engineering at Rensselaer. "In order to understand how and why this all happens, we first need to know their structure. And today, at least for the simplest glycosaminoglycan structure, we can now do this."

The first glycosaminoglycan sequenced was obtained from bikunin. Bikunin is a proteoglycan, a protein to which a single glycosaminoglycan chain is attached. Unlike less sophisticated carbohydrate biopolymers, such as starch and cellulose, the proteoglycans are decorated with structurally complex carbohydrates that enable them to perform more sophisticated and defined roles in the body. Bikunin, for example, is a natural anti-inflammatory that is used as a drug for the treatment of acute pancreatitis in Japan. It has the simplest chemical structure of any proteoglycan. Linhardt views the discovery of the structure of bikuin as the first step on the ladder to the discovery of the structure of more complex proteoglycans.

"The first genome sequences of DNA were on the simplest organisms such as bacteria. Once the technology was developed it ultimately led to the sequencing of the human genome," he said. "In our efforts to sequence carbohydrate biopolymers we don't yet know if the defined structure we observe for this simple protoglycan will hold for much more complex proteoglycans."

But, looking for structure in more complex proteoglycans will be among the next steps in the research for Linhardt and his team. The search for structure could help put to rest a long-running debate in the scientific community as to whether complex carbohydrate biopolymers require a defined structure to function.

"Despite all that is known about glycan formation, our understanding has not yet been deep enough to infer sequence or even determine if sequence occurs," Linhardt said. "These findings represent a new way of looking at these complex biomolecules as ordered structures."

Linhardt's research into carbohydrate sequencing began 30 years ago. In his previous work, he determined that some order existed in at least a portion of some carbohydrate biopolymers, but it did not represent the entire finished puzzle.

"Previously, we could see a pattern, but we could not see if all the chains were playing the same music. The tools did not yet exist. Now we can recognize it as a symphony."

To uncover the entire structure, Linhardt and his team, which was led by his doctoral student Mellisa Ly, borrowed a technique from the field of protein research called the proteomics top-down approach. As opposed to the bottom-up approach that first breaks apart a complex biopolymer into pieces and then rebuilds it piece by piece like a jigsaw puzzle, the top-down approach used by Linhardt and colleagues allows the researcher to picture the whole intact puzzle. This can only be accomplished with some of the most sophisticated technology available to the scientific community today, including very high-powered mass spectrometers.

Linhardt used a mass spectrometer located in the Rensselaer Center for Biotechnology and Interdisciplinary Studies (CBIS) to make his initial discoveries, and had these results independently confirmed on a separate and higher-level spectrometer at the University of Georgia. Mass spectrometers break down a molecule into separate charged particles or ions. These ions can then be categorized and analyzed based on their mass-to-charge ratio. These ratios then allow for sequencing of the entire molecule.

"This was truly the convergence of really sophisticated spectroscopy and its application to biology," Linhardt said. "We were fortunate to have a lot of time to play with the instrument at CBIS to understand its capabilities."

Beyond the technology it also took faith and determination. According to Linhardt, "It takes a student that is willing to try something even when the odds are pretty low. If it doesn't work, you make incremental progress. If it does work, you can make a great discovery. But, from the beginning you need to be a believer that it is worth taking the chance because it takes a lot of hard work in the lab."

And the odds weren't in Linhardt's favor. Despite being the most simple of proteoglycans, there were still 290 billion different possible sequences for the molecule.

"The first sample we looked at, we got the structure," Linhardt said. "In the end we did 15 chains and they all came back playing the same exact symphony."

The research is funded by the National Institutes of Health.

Linhardt and Ly were joined in the research by Tatiana Laremore of Rensselaer; Franklin Leach and Jonathan Amster of the University of Georgia; and Toshihiko Toida of Chiba University in Japan.

Journal Reference:

1. Mellisa Ly, Franklin E Leach, Tatiana N Laremore, Toshihiko Toida, I Jonathan Amster, Robert J Linhardt. The proteoglycan bikunin has a defined sequence. Nature Chemical Biology, 2011; DOI: 10.1038/nchembio.673

Courtesy: ScienceDaily

Compound Kills Highly Contagious Flu Strain by Activating Antiviral Protein

A compound tested by UT Southwestern Medical Center investigators destroys several viruses, including the deadly Spanish flu that killed an estimated 30 million people in the worldwide pandemic of 1918.

This lead compound -- which acts by increasing the levels of a human antiviral protein -- could potentially be developed into a new drug to combat the flu, a virus that tends to mutate into strains resistant to anti-influenza drugs.

"The virus is 'smart' enough to bypass inhibitors or vaccines sometimes. Therefore, there is a need for alternative strategies. Current drugs act on the virus, but here we are uplifting a host/human antiviral response at the cellular level," said Dr. Beatriz Fontoura, associate professor of cell biology and senior author of the study available online in Nature Chemical Biology.

According to National Institutes of Health, influenza hospitalizes more than 200,000 people in the U.S. each year, with about 36,000 fatalities related to the illness. Worldwide, flu kills about 500,000 people annually.

In the latest cell testing, the compound successfully knocked out three types of influenza as well as a smallpox-related virus and an animal virus. Because of the highly contagious nature of the 1918 flu, those tests took place at Mount Sinai School of Medicine in New York, one of the few places that stores and runs tests on that flu strain.

The compound is among others that the research team is testing that induce an infection-fighting human protein called REDD1. Until this study, researchers had not demonstrated that REDD1 had this important antiviral function.

"We've discovered that REDD1 is a key human barrier for infection," said Dr. Fontoura, "Interestingly, REDD1 inhibits a signaling pathway that regulates cell proliferation and cancer."

The UT Southwestern-led research team tested 200,000 compounds for those that would inhibit flu virus infection. A total of 71 were identified.

Using the two most promising compounds, researchers at UT Southwestern and colleagues at Mount Sinai next will work to strengthen their potencies for further testing. Dr. Fontoura said it can take more than 10 years before successful compounds are developed into drugs.

UT Southwestern researchers involved in the study were lead author Miguel Mata and Neal Satterly, both graduate students in Dr. Fontoura's laboratory; Dr. Doug Frantz, former assistant professor of biochemistry; Shuguang Wei, a senior researcher in biochemistry; Dr. Noelle Williams, associate professor of biochemistry; Samuel Pena-Llopis, assistant instructor in developmental biology; Dr. James Brugarolas, assistant professor of internal medicine; Dr. Christian Forst, assistant professor of clinical sciences; Dr. Michael White, professor of cell biology; and Dr. Michael Roth, professor of biochemistry.

The research was supported by nine National Institutes of Health grants and by the Diane and Hal Brierley Distinguished Chair Fund.

Journal Reference:

1. Miguel A Mata, Neal Satterly, Gijs A Versteeg, Doug Frantz, Shuguang Wei, Noelle Williams, Mirco Schmolke, Samuel Peña-Llopis, James Brugarolas, Christian V Forst, Michael A White, Adolfo García-Sastre, Michael G Roth, Beatriz M A Fontoura. Chemical inhibition of RNA viruses reveals REDD1 as a host defense factor. Nature Chemical Biology, 2011; 7 (10): 712 DOI: 10.1038/nchembio.645

Courtesy: ScienceDaily

Edible Carbon Dioxide Sponge: All-Natural Nanostructures Could Address Pressing Environmental Problem

A year ago Northwestern University chemists published their recipe for a new class of nanostructures made of sugar, salt and alcohol. Now, the same team has discovered the edible compounds can efficiently detect, capture and store carbon dioxide. And the compounds themselves are carbon-neutral.

The porous crystals -- known as metal-organic frameworks (MOFs) -- are made from all-natural ingredients and are simple to prepare, giving them a huge advantage over other MOFs. Conventional MOFs, which also are effective at adsorbing carbon dioxide, are usually prepared from materials derived from crude oil and often incorporate toxic heavy metals.

Other features of the Northwestern MOFs are they turn red when completely full of carbon dioxide, and the carbon capture process is reversible.

The findings, made by scientists working in the laboratory of Sir Fraser Stoddart, Board of Trustees Professor of Chemistry in the Weinberg College of Arts and Sciences, are published in the Journal of the American Chemical Society (JACS).

"We are able to take molecules that are themselves sourced from atmospheric carbon, through photosynthesis, and use them to capture even more carbon dioxide," said Ross S. Forgan, a co-author of the study and a postdoctoral fellow in Stoddart's laboratory. "By preparing our MOFs from naturally derived ingredients, we are not only making materials that are entirely nontoxic, but we are also cutting down on the carbon dioxide emissions associated with their manufacture."

The main component, gamma-cyclodextrin, is a naturally occurring biorenewable sugar molecule that is derived from cornstarch.

The sugar molecules are held in place by metals taken from salts such as potassium benzoate or rubidium hydroxide, and it is the precise arrangement of the sugars in the crystals that is vital to their successful capture of carbon dioxide.

"It turns out that a fairly unexpected event occurs when you put that many sugars next to each other in an alkaline environment -- they start reacting with carbon dioxide in a process akin to carbon fixation, which is how sugars are made in the first place," said Jeremiah J. Gassensmith, lead author of the paper and also a postdoctoral fellow in Stoddart's laboratory. "The reaction leads to the carbon dioxide being tightly bound inside the crystals, but we can still recover it at a later date very simply."

The fact that the carbon dioxide reacts with the MOF, an unusual occurrence, led to a simple method of detecting when the crystals have reached full capacity. The researchers place an indicator molecule, which detects changes in pH by changing its color, inside each crystal. When the yellow crystals of the MOFs are full of carbon dioxide they turn red.

The simplicity of the new MOFs, allied with their low cost and green credentials, have marked them as candidates for further commercialization. Ronald A. Smaldone, also a postdoctoral fellow in Stoddart's group and a co-author of the paper, added, "I think this is a remarkable demonstration of how simple chemistry can be successfully applied to relevant problems like carbon capture and sensor technology."

The National Science Foundation, the U.S. Department of Energy, the Engineering and Physical Sciences Research Council in the U.K., the King Abdulaziz City of Science and Technology (KACST) in Saudi Arabia and the Korea Advanced Institute of Science and Technology (KAIST) in Korea supported the research.

Journal Reference:

1. Jeremiah J. Gassensmith, Hiroyasu Furukawa, Ronald A. Smaldone, Ross S. Forgan, Youssry Y. Botros, Omar M. Yaghi, J. Fraser Stoddart. Strong and Reversible Binding of Carbon Dioxide in a Green Metal–Organic Framework. Journal of the American Chemical Society, 2011; 110913144109022 DOI: 10.1021/ja206525x

Courtesy: ScienceDaily

Targeting HIV's Sugar Coating: New Microbicide May Block AIDS Virus from Infecting Cells

University of Utah researchers have discovered a new class of compounds that stick to the sugary coating of the AIDS virus and inhibit it from infecting cells -- an early step toward a new treatment to prevent sexual transmission of the virus.

Development and laboratory testing of the potential new microbicide to prevent human immunodeficiency virus infection is outlined in a study set for online publication in the journal Molecular Pharmaceutics.

Despite years of research, there is only one effective microbicide to prevent sexual transmission of HIV, which causes AIDS, or acquired immune deficiency syndrome. Microbicide development has focused on gels and other treatments that would be applied vaginally by women, particularly in Africa and other developing regions.

To establish infection, HIV must first enter the cells of a host organism and then take control of the cells' replication machinery to make copies of itself. Those HIV copies in turn infect other cells. These two steps of the HIV life cycle, known as viral entry and viral replication, each provide a potential target for anti-AIDS medicines.

"Most of the anti-HIV drugs in clinical trials target the machinery involved in viral replication," says the study's senior author, Patrick F. Kiser, associate professor of bioengineering and adjunct associate professor of pharmaceutics and pharmaceutical chemistry at the University of Utah.

"There is a gap in the HIV treatment pipeline for cost-effective and mass-producible viral entry inhibitors that can inactivate the virus before it has a chance to interact with target cells," he says.

Kiser conducted the study with Alamelu Mahalingham, a University of Utah graduate student in pharmaceutics and pharmaceutical chemistry; Anthony Geonnotti of Duke University Medical Center in Durham, N.C.; and Jan Balzarini of Catholic University of Leuven in Belgium.

The research was funded by the National Institutes of Health, the Bill and Melinda Gates Foundation, the Catholic University of Leuven, Belgium, and the Fund for Scientific Research, also in Belgium.

Synthetic Lectins Inhibit HIV from Entering Cells

Lectins are a group of molecules found throughout nature that interact and bind with specific sugars. HIV is coated with sugars that help to hide it from the immune system. Previous research has shown that lectins derived from plants and bacteria inhibit the entry of HIV into cells by binding to sugars found on the envelope coating the virus.

However, the cost of producing and purifying natural lectins is prohibitively high. So Kiser and his colleagues developed and evaluated the anti-HIV activity of synthetic lectins based on a compound called benzoboroxole, or BzB, which sticks to sugars found on the HIV envelope.

Kiser and his colleagues found that these BzB-based lectins were capable of binding to sugar residues on HIV, but the bond was too weak to be useful. To improve binding, they developed polymers of the synthetic lectins. The polymers are larger molecules made up of repeating subunits, which contained multiple BzB binding sites. The researchers discovered that increasing the number and density of BzB binding sites on the synthetic lectins made the substances better able to bind to the AIDS virus and thus have increased antiviral activity.

"The polymers we made are so active against HIV that dissolving about one sugar cube's weight of the benzoboroxole polymer in a bath tub of water would be enough to inhibit HIV infection in cells," says Kiser.

Depending on the strain, HIV displays significant variations in its viral envelope, so it is important to evaluate the efficacy of any potential new treatment against many different HIV strains.

Kiser and his colleagues found that their synthetic lectins not only showed similar activity across a broad spectrum of HIV strains, but also were specific to HIV and didn't affect other viruses with envelopes.

The scientists also tested the anti-HIV activity of the synthetic lectins in the presence of fructose, a sugar present in semen, which could potentially compromise the activity of lectin-based drugs because it presents an alternative binding site. However, the researchers found that the antiviral activity of the synthetic lectins was fully preserved in the presence of fructose.

"The characteristics of an ideal anti-HIV microbicide include potency, broad-spectrum activity, selective inhibition, mass producibility and biocompatibility," says Kiser. "These benzoboroxole-based synthetic lectins seem to meet all of those criteria and present an affordable and scalable potential intervention for preventing sexual transmission in regions where HIV is pandemic."

Kiser says future research will focus on evaluating the ability of synthetic lectins to prevent HIV transmission in tissues taken from the human body, with later testing in primates. Kiser and his colleagues are also developing a gel form of the polymers, which could be used as a topical treatment for preventing sexual HIV transmission.

Journal Reference:

1. Alamelu Mahalingam, Anthony R Geonnotti, Jan Balzarini, Patrick Franklin Kiser. Activity and Safety of Synthetic Lectins Based on Benzoboroxole-Functionalized Polymers for Inhibition of HIV Entry. Molecular Pharmaceutics, 2011; 110831135436035 DOI: 10.1021/mp2002957

Courtesy: ScienceDaily

Scientists Take First Step Towards Creating 'Inorganic Life'

Scientists at the University of Glasgow say they have taken their first tentative steps towards creating 'life' from inorganic chemicals potentially defining the new area of 'inorganic biology'.

Professor Lee Cronin, Gardiner Chair of Chemistry in the College of Science and Engineering, and his team have demonstrated a new way of making inorganic-chemical-cells or iCHELLs.

Prof Cronin said: "All life on earth is based on organic biology (i.e. carbon in the form of amino acids, nucleotides, and sugars, etc.) but the inorganic world is considered to be inanimate.

"What we are trying do is create self-replicating, evolving inorganic cells that would essentially be alive. You could call it inorganic biology."

The cells can be compartmentalised by creating internal membranes that control the passage of materials and energy through them, meaning several chemical processes can be isolated within the same cell -- just like biological cells.

The researchers say the cells, which can also store electricity, could potentially be used in all sorts of applications in medicine, as sensors or to confine chemical reactions.

The research is part of a project by Prof Cronin to demonstrate that inorganic chemical compounds are capable of self-replicating and evolving -- just as organic, biological carbon-based cells do.

The research into creating 'inorganic life' is in its earliest stages, but Prof Cronin believes it is entirely feasible.

Prof Cronin said: "The grand aim is to construct complex chemical cells with life-like properties that could help us understand how life emerged and also to use this approach to define a new technology based upon evolution in the material world -- a kind of inorganic living technology.

"Bacteria are essentially single-cell micro-organisms made from organic chemicals, so why can't we make micro-organisms from inorganic chemicals and allow them to evolve?

"If successful this would give us some incredible insights into evolution and show that it's not just a biological process. It would also mean that we would have proven that non carbon-based life could exist and totally redefine our ideas of design."

The paper is published in the journal Angewandte Chemie.

Journal Reference:

1. Geoffrey J. T. Cooper, Philip J. Kitson, Ross Winter, Michele Zagnoni, De-Liang Long, Leroy Cronin. Modular Redox-Active Inorganic Chemical Cells: iCHELLs. Angewandte Chemie International Edition, 2011; DOI: 10.1002/anie.201105068

Courtesy: ScienceDaily

Potential Molecular Target to Prevent Growth of Cancer Cells Identified

Researchers have shown for the first time that the protein fortilin promotes growth of cancer cells by binding to and rendering inert protein p53, a known tumor suppressor. This finding by researchers at the University of Texas Medical Branch may lead to treatments for a range of cancers and atherosclerosis, which p53 also helps prevent, and appears in the current print issue of the Journal of Biological Chemistry.

"The p53 protein is a critical defense against cancer because it activates genes that induce apoptosis, or the death of cells. However, p53 can be made powerless by mutations and inhibitors like fortilin," said Dr. Ken Fujise, lead author of the study and director, Division of Cardiology at UTMB.

Fortilin, an amino acid polypeptide protein, works in direct opposition to p53, protecting cells from apoptosis. Fujise discovered fortilin in 2000 and the protein has become a central focus of his research. This study marks the first time that scientists have been able to show the exact mechanism whereby fortilin exerts its anti-apoptotic activity.

Fujise and his team used cell cultures and animal models to show that fortilin binds to and inhibits p53, preventing it from activating genes, such as BAX and Noxa, that facilitate cell death. Thus, cells that would be killed are allowed to proliferate.

"When normal cells become cancer cells, our bodies' natural biological response is to activate p53, which eliminates the hopelessly damaged cells," said Fujise. "This process explains why the majority of people are able to stay cancer-free for most of their lives. Conversely, mutated p53 genes are seen in more than half of all human cancers, making them the most frequently observed genetic abnormality in cancer."

According to Fujise, upon further research and validation of the biological mechanism described in this study, scientists can begin exploring compounds that could modulate fortilin's activity on p53.

Such a compound would be a powerful chemotherapy agent and, because p53 inhibition has also been associated with atherosclerosis, could also protect against coronary disease and its many complications, including heart attack and stroke.

"Though we are in the early stages of this research, once screening for compounds is initiated, we could have a potential new drug to investigate in a very short period of time," said Fujise. With the support of National Institutes of Health high-throughput screening programs, which make it possible to screen very large numbers of compounds against a drug target, the process of identifying a new drug could potentially be shortened to months rather than years, he added.

Other authors include scientists at UTMB and other institutions: Yanjie Chen, Takayuki Fujita, Di Zhang, Hung Doan, Decha Pinkaew, Zhihe Liu, Jiaxin Wu, Yuichi Koide, Andrew Chiu, Curtis Chen Jun Lin, Jui-Yoa Chang; and Ke-He Ruan.

The study was supported in part by the National Institutes of Health, the American Heart Association, and MacDonald General Research Fund.

Journal Reference:

1. Y. Chen, T. Fujita, D. Zhang, H. Doan, D. Pinkaew, Z. Liu, J. Wu, Y. Koide, A. Chiu, C. C.-J. Lin, J.-Y. Chang, K.-H. Ruan, K. Fujise. Physical and Functional Antagonism between Tumor Suppressor Protein p53 and Fortilin, an Anti-apoptotic Protein. Journal of Biological Chemistry, 2011; 286 (37): 32575 DOI: 10.1074/jbc.M110.217836

Courtesy: ScienceDaily

World-First Viral Therapy Trial in Cancer Patients

Researchers from the Ottawa Hospital Research Institute (OHRI), the University of Ottawa (uOttawa), Jennerex Inc. and several other institutions have just reported promising results of a world-first cancer therapy trial in journal Nature. The trial is the first to show that an intravenously-delivered viral therapy can consistently infect and spread within tumours without harming normal tissues in humans. It is also the first to show tumour-selective expression of a foreign gene after intravenous delivery.

The trial involved 23 patients (including seven at The Ottawa Hospital), all with advanced cancers that had spread to multiple organs and failed to respond to standard treatments. The patients received a single intravenous infusion of a virus called JX-594, at one of five dose levels, and biopsies were obtained eight to 10 days later. Seven of eight patients (87 per cent) in the two highest dose groups had evidence of viral replication in their tumour, but not in normal tissues. All of these patients also showed tumour-selective expression of a foreign gene that was engineered into the virus to help with detection. The virus was well tolerated at all dose levels, with the most common side effect being mild to moderate flu-like symptoms that lasted less than one day.

"We are very excited because this is the first time in medical history that a viral therapy has been shown to consistently and selectively replicate in cancer tissue after intravenous infusion in humans," said Dr. John Bell, a Senior Scientist at OHRI, Professor of Medicine at uOttawa and senior co-author on the publication. "Intravenous delivery is crucial for cancer treatment because it allows us to target tumours throughout the body as opposed to just those that we can directly inject. The study is also important because it shows that we can use this approach to selectively express foreign genes in tumours, opening the door to a whole new suite of targeted cancer therapies."

Dr. Bell and his team have been investigating cancer-fighting (oncolytic) viruses at OHRI for more than 10 years. JX-594 was developed in partnership with Jennerex Inc., a biotherpeutics company co-founded by Dr. Bell in Ottawa and Dr. David Kirn in San Francisco. JX-594 is derived from a strain of vaccinia virus that has been used extensively as a live vaccine against smallpox. It has a natural ability to replicate preferentially in cancer cells, but it has also been genetically engineered to enhance its anti-cancer properties.

"Oncolytic viruses are unique because they can attack tumours in multiple ways, they have very mild side effects compared to other treatments, and they can be easily customized for different kinds of cancer," said Dr. Bell. "We're still in the early stages of testing these viruses in patients, but I believe that someday, viruses and other biological therapies could truly transform our approach for treating cancer."

Although the current trial was designed primarily to assess safety and delivery of JX-594, anti-tumour activity was also evaluated. Six of eight patients (75%) in the two highest dose groups experienced a shrinking or stabilization of their tumour, while those in lower dose groups were less likely to experience this effect.

"These results are promising, especially for such an early-stage trial, with only one dose of therapy," said Dr. Bell. "But of course, we will need to do more trials to know if this virus can truly make a difference for patients. We are working hard to get these trials started, and at the same time, we are also working in the laboratory to advance our understanding of these viruses and figure out how best to use them."

This research was supported by Jennerex Inc., the Terry Fox Foundation, the Canadian Institutes of Health Research, the Ontario Institute for Cancer Research, The Ottawa Hospital Foundation, the Canada Foundation for Innovation, the Natural Sciences and Engineering Research Council of Canada and the Republic of Korea. OHRI / uOttawa authors on the paper include Dr. John Bell, Dr. Derek Jonker, Dr. Laura Chow, Dr. Fabrice Le Boeuf, Joe Burns, Laura Evgin, Naomi De Silva, Sara Cvancic, Dr. Kelley Parato, Dr. Jean-Simon Diallo and Dr. Manijeh Daneshmand, as well as alumnus Dr. Caroline Breitbach.

Journal Reference:

1. Caroline J. Breitbach, James Burke, Derek Jonker, Joe Stephenson, Andrew R. Haas, Laura Q. M. Chow, Jorge Nieva, Tae-Ho Hwang, Anne Moon, Richard Patt, Adina Pelusio, Fabrice Le Boeuf, Joe Burns, Laura Evgin, Naomi De Silva, Sara Cvancic, Terri Robertson, Ji-Eun Je, Yeon-Sook Lee, Kelley Parato, Jean-Simon Diallo, Aaron Fenster, Manijeh Daneshmand, John C. Bell, David H. Kirn. Intravenous delivery of a multi-mechanistic cancer-targeted oncolytic poxvirus in humans. Nature, 2011; 477 (7362): 99 DOI: 10.1038/nature10358

Courtesy: ScienceDaily

Nanosensors Made from DNA May Light Path to New Cancer Tests and Drugs

Sensors made from custom DNA molecules could be used to personalize cancer treatments and monitor the quality of stem cells, according to an international team of researchers led by scientists at UC Santa Barbara and the University of Rome Tor Vergata.

The new nanosensors can quickly detect a broad class of proteins called transcription factors, which serve as the master control switches of life. The research is described in an article published in Journal of the American Chemical Society.

"The fate of our cells is controlled by thousands of different proteins, called transcription factors," said Alexis Vallée-Bélisle, a postdoctoral researcher in UCSB's Department of Chemistry and Biochemistry, who led the study. "The role of these proteins is to read the genome and translate it into instructions for the synthesis of the various molecules that compose and control the cell. Transcription factors act a little bit like the 'settings' of our cells, just like the settings on our phones or computers. What our sensors do is read those settings."

When scientists take stem cells and turn them into specialized cells, they do so by changing the levels of a few transcription factors, he explained. This process is called cell reprogramming. "Our sensors monitor transcription factor activities, and could be used to make sure that stem cells have been properly reprogrammed," said Vallée-Bélisle. "They could also be used to determine which transcription factors are activated or repressed in a patient's cancer cells, thus enabling physicians to use the right combination of drugs for each patient."

Andrew Bonham, a postdoctoral scholar at UCSB and co-first author of the study, explained that many labs have invented ways to read transcription factors; however, this team's approach is very quick and convenient. "In most labs, researchers spend hours extracting the proteins from cells before analyzing them," said Bonham. "With the new sensors, we just mash the cells up, put the sensors in, and measure the level of fluorescence of the sample."

This international research effort -- organized by senior authors Kevin Plaxco, professor in UCSB's Department of Chemistry and Biochemistry, and Francesco Ricci, professor at the University of Rome, Tor Vergata -- started when Ricci realized that all of the information necessary to detect transcription factor activities is already encrypted in the human genome, and could be used to build sensors. "Upon activation, these thousands of different transcription factors bind to their own specific target DNA sequence," said Ricci. "We use these sequences as a starting point to build our new nanosensors."

The key breakthrough underlying this new technology came from studies of the natural biosensors inside cells. "All creatures, from bacteria to humans, monitor their environments using 'biomolecular switches' -- shape-changing molecules made from RNA or proteins," said Plaxco. "For example, in our sinuses, there are millions of receptor proteins that detect different odor molecules by switching from an 'off state' to an 'on state.' The beauty of these switches is that they are small enough to operate inside a cell, and specific enough to work in the very complex environments found there."

Inspired by the efficiency of these natural nanosensors, the research group teamed with Norbert Reich, also a professor in UCSB's Department of Chemistry and Biochemistry, to build synthetic switching nanosensors using DNA, rather than proteins or RNA.

Specifically, the team re-engineered three naturally occurring DNA sequences, each recognizing a different transcription factor, into molecular switches that become fluorescent when they bind to their intended targets. Using these nanometer-scale sensors, the researchers could determine transcription factor activity directly in cellular extracts by simply measuring their fluorescence level.

The researchers believe that this strategy will ultimately allow biologists to monitor the activation of thousands of transcription factors, leading to a better understanding of the mechanisms underlying cell division and development. "Alternatively, since these nanosensors work directly in biological samples, we also believe that they could be used to screen and test new drugs that could, for example, inhibit transcription-factor binding activity responsible for the growth of tumor cells," said Plaxco.

This work was funded by the National Institute of Health, the Fond Québécois de la Recherche sur la Nature et les Technologies, the Italian Ministry of University and Research (MIUR) project "Futuro in Ricerca," and the Tri-County Blood Bank Santa Barbara Foundation.

Journal Reference:

1. Alexis Vallée-Bélisle, Andrew J. Bonham, Norbert O. Reich, Francesco Ricci, Kevin W. Plaxco. Transcription Factor Beacons for the Quantitative Detection of DNA Binding Activity. Journal of the American Chemical Society, 2011; 133 (35): 13836 DOI: 10.1021/ja204775k

Courtesy: ScienceDaily

Doctors' and Nurses' Hospital Uniforms Contain Dangerous Bacteria a Majority of the Time, Study Shows

More than 60 percent of hospital nurses' and doctors' uniforms tested positive for potentially dangerous bacteria, according to a study published in the September issue of the American Journal of Infection Control, the official publication of APIC -- the Association for Professionals in Infection Control and Epidemiology.

A team of researchers led by Yonit Wiener-Well, MD, from the Shaare Zedek Medical Center in Jerusalem, Israel, collected swab samples from three parts of the uniforms of 75 registered nurses (RNs) and 60 medical doctors (MDs) by pressing standard blood agar plates at the abdominal zone, sleeves' ends and pockets.

The researchers at this 550-bed, university-affiliated hospital found that exactly half of all the cultures taken, representing 65 percent of the RN uniforms and 60 percent of the MD uniforms, harbored pathogens. Of those, 21 cultures from RN uniforms and six cultures from MD uniforms contained multi-drug resistant pathogens, including eight cultures that grew methicillin-resistant Staphylococcus aureus (MRSA). Although the uniforms themselves may not pose a direct risk of disease transmission, these results indicate a prevalence of antibiotic resistant strains in close proximity to hospitalized patients.

"It is important to put these study results into perspective," said APIC 2011 President Russell Olmsted, MPH, CIC. "Any clothing that is worn by humans will become contaminated with microorganisms. The cornerstone of infection prevention remains the use of hand hygiene to prevent the movement of microbes from these surfaces to patients."

"New evidence such as this study by Dr. Wiener-Well is helpful to improve the understanding of potential sources of contamination but, as is true for many studies, it raises additional questions that need to be investigated," added Olmsted.

According to the World Health Organization, the risk of healthcare-associated infection (HAI) in some developing countries is as much as 20 times higher than in developed countries. Even in hospitals in developed countries like Israel, the site of this investigation, and the U.S., HAIs occur too often, can be deadly, and are expensive to treat. HAI prevention is therefore the best approach for patient safety. Infection preventionists, in collaboration with direct care providers, can prevent more than half of HAIs by applying proven prevention practices as part of a comprehensive infection prevention and control program.

Journal Reference:

1. Yonit Wiener-Well, Margalit Galuty, Bernard Rudensky, Yechiel Schlesinger, Denise Attias, Amos M. Yinnon. Nursing and physician attire as possible source of nosocomial infections. American Journal of Infection Control, 2011; 39 (7): 555 DOI: 10.1016/j.ajic.2010.12.016

Courtesy: ScienceDaily

New Strategy for Overcoming Resistance to Targeted Cancer Drug

Scientists at Dana-Farber Cancer Institute and colleagues overseas have discovered a pair of backup circuits in cancer cells that enable the cells to dodge the effect of a widely used cancer drug. Jamming those circuits with targeted therapies may heighten or restore the drug's potency, according to a study published in the Sept. 7 issue of Science Translational Medicine.

The research focused on the drug cetuximab, an antibody that interferes with cancer cell growth by blocking a structure known as the epidermal growth factor receptor (EGFR). Cetuximab is effective in many patients with colorectal cancer or squamous cell cancer of the head and neck, but the benefits rarely last longer than a year, and some patients receive no benefit from the drug.

Until now, scientists haven't known why cancers that initially respond to cetuximab become resistant to it, or how to overcome such resistance.

In the new study, researchers led by Pasi Janne, MD, PhD, of Dana-Farber and Kimio Yonesaka, MD, PhD, formerly of Dana-Farber and now at Kinki University School of Medicine, in Osaka, Japan, found that in some cetuximab-resistant cancer cells, a protein known as ERBB2 was actively sending "grow" signals, circumventing the "stop growing" signals triggered by cetuximab. The researchers discovered that ERBB2's activity sprang from an oversupply of the protein's parent gene, Her2/neu, or by a related protein, ERBB3, when prompted by high levels of the protein heregulin. In both cases, the new growth messages are unaffected by cetuximab.

"ERBB2 activates a critical signaling pathway that is not normally blocked by cetuximab, and in this way subverts cetuximab's function," says Janne, the study's co-senior author with Kazuhiko Nakagawa, MD, PhD, of Kinki University. "Because ERBB2 isn't affected by cetuximab, this is an easy way for cancers to become resistant to the drug."

The findings suggest that combining cetuximab with ERBB2-inhibiting drugs could be an effective therapy for cancers that are cetuximab-resistant from the start or for those that become resistant over time, the study authors say. Several such inhibitors have already been approved, while others are undergoing clinical study.

"We hope the findings of our study will inspire the development of clinical trials aimed at overcoming cetuximab resistance," Yonesaka remarks. "We've identified biomarkers that can be used to select cetuximab-resistant patients who may benefit from a combination of cetuximab and ERBB2 inhibitors."

Janne estimates that up to 40 percent of colorectal cancers are cetuximab-resistant when first diagnosed. He notes that although the ERBB2 pathway may be responsible for many cases of cetuximab resistance, there are undoubtedly other pathways, yet to be discovered, that play a similar role. Further research is needed to confirm ERBB2's role in cetuximab resistance and to develop strategies for testing ERBB2 inhibitors and cetuximab in clinical trials.

Funding for the study was provided by grants from the National Institutes of Health, the American Cancer Society, the William Randolph Hearst Foundation, and the Hazel and Samuel Bellin research fund.

Co-authors of the paper include Kreshnik Zejnullahu, Dalia Ercan, Andrew Rogers, Juliet Philips, MS, Jason Sun, Takafumi Okabe, MD, PhD, Jeffrey Swanson, MD, and Ramesh Shivdasani, MD, PhD, Dana-Farber; Isamu Okamoto, MD, PhD, Taroh Satoh, MD, Masayuki Takeda, MD, PhD, Yasuhito Fujisaka, MD, Toshio Shimizu, MD, PhD, Osamu Maenishi, Hiroyuki Itoh, MD, Kiyotaka Okuno, MD, Minoru Takada, MD, Masahiro Fukuoka, MD, and Kazuto Nishio, MD, PhD, Kinki University, Osaka, Japan; Federico Cappuzzo, MD, Massimo Roncalli, MD, and Annarita Destro, PhD, Instituto Clinico Humanitas, Rozzano, Italy; John Souglakos, MD, PhD, University of Crete, Heraklion, Greece; Yonggon Cho, and Marileila Varella-Garcia, University of Colorado Cancer Center, Denver; Koichi Taira, MD, and Koji Takeda, MD, Osaka City General Hospital, Japan; and Eugene Lifshits and Jeffrey Engelman, MD, PhD, Massachusetts General Hospital.

Journal Reference:

1. Kimio Yonesaka, Kreshnik Zejnullahu, Isamu Okamoto, Taroh Satoh, Federico Cappuzzo, John Souglakos, Dalia Ercan, Andrew Rogers, Massimo Roncalli, Masayuki Takeda, Yasuhito Fujisaka, Juliet Philips, Toshio Shimizu, Osamu Maenishi, Yonggon Cho, Jason Sun, Annarita Destro, Koichi Taira, Koji Takeda, Takafumi Okabe, Jeffrey Swanson, Hiroyuki Itoh, Minoru Takada, Eugene Lifshits, Kiyotaka Okuno, Jeffrey A. Engelman, Ramesh A. Shivdasani, Kazuto Nishio, Masahiro Fukuoka, Marileila Varella-Garcia, Kazuhiko Nakagawa, Pasi A. Jänne. Activation of ERBB2 Signaling Causes Resistance to the EGFR-Directed Therapeutic Antibody Cetuximab. Science Translational Medicine, 2011; 3 (99): 99ra86 DOI: 10.1126/scitranslmed.3002442

Courtesy: ScienceDaily

Scientists Pinpoint Shape-Shifting Mechanism Critical to Protein Signaling

In a joint study, scientists from the California and Florida campuses of The Scripps Research Institute have shown that changes in a protein's structure can change its signaling function and they have pinpointed the precise regions where those changes take place.

The new findings could help provide a much clearer picture of potential drugs that would be both effective and highly specific in their biological actions.

The study, led by Patrick Griffin of Scripps Florida and Raymond Stevens of Scripps California, was published in a recent edition of the journal Structure.

The new study focuses on the β2-adrenergic receptor, a member of the G protein-coupled receptor family. G protein-coupled receptors convert extracellular stimuli into intracellular signals through various pathways. Approximately one third of currently marketed drugs (including for diabetes and heart disease) target these receptors.

Scientists have known that when specific regions of the receptor are activated by neurotransmitters or hormones, the structural arrangement (conformation) of the receptor is changed along with its function.

"While it's accepted that these receptors adopt multiple conformations and that each conformation triggers a specific type of signaling, the molecular mechanism behind that flexibility has been something of a black box," said Griffin, who is chair of the Scripps Research Department of Molecular Therapeutics and director of the Scripps Florida Translational Research Institute. "Our findings shed significant light to it."

The study describes in structural detail the various regions of the receptor that are involved in the changes brought about by selective ligands (ligands are molecules that bind to proteins to form an active complex), which, like a rheostat, run the gamut among activating the receptor, shutting it down, and reversing its function, as well as producing various states in between.

To achieve the results described in the study, the team used hydrogen-deuterium (HDX) mass spectrometry to measure the impact of interaction of various functionally selective ligands with the β2-adrenergic receptor. A mass spectrometer determines the mass of fragments from the receptor by measuring the mass-to-charge ratio of their ions. HDX has been used to examine changes in the shape of proteins and how these shape changes relate to protein function. The approach is often used to characterize protein-protein interactions that are critical for signal transduction in cells and to study protein-folding pathways that are critical to cell survival.

"At this early stage in understanding GPCR structure and function, it is important to view the entire receptor in combination with probing very specific regions," said Stevens, who is a professor in the Scripps Research Department of Molecular Biology. "Hydrogen-deuterium exchange mass spectrometry has the right timescale and resolution to asked important questions about complete receptor conformations in regards to different pharmacological ligand binding. The HDX data combined with the structural data emerging will really help everyone more fully understand how these receptors work."

"Using the HDX technology we can study the intact receptor upon interaction with ligands and pinpoint regions of the receptor that have undergone change in position or flexibility," Griffin said. "By studying a set of ligands one can start to develop patterns that are tied to activation of the receptor or shutting it down. Once we get a picture of what a functional ligand looks like, it might be possible to develop a drug to produce a highly selective therapeutic effect."

The lead author of the study, "Ligand-Dependent Perturbation of the Conformational Ensemble for the GPCR b2 Adrenergic Receptor Revealed by HDX," is Graham M. West of Scripps Research. Other authors include Ellen Y.T. Chien, Jovylyn Gatchalian, and Michael J. Chalmers of Scripps Research, and Vsevolod Katritch of the University of California, San Diego.

The study was supported by the National Institutes of Health.

Journal Reference:

1. Graham M. West, Ellen Y.T. Chien, Vsevolod Katritch, Jovylyn Gatchalian, Michael J. Chalmers, Raymond C. Stevens, Patrick R. Griffin. Ligand-Dependent Perturbation of the Conformational Ensemble for the GPCR β2 Adrenergic Receptor Revealed by HDX. Structure, 2011; DOI: 10.1016/j.str.2011.08.001

Courtesy: ScienceDaily

Cognitive Changes May Predict Alzheimer's Disease Development More Accurately Than Biomarkers

Compared with changes in biomarkers, changes in cognitive abilities appear to be stronger predictors of whether an individual with mild cognitive impairment (MCI) will develop Alzheimer's disease, according to a report in the September issue of Archives of General Psychiatry, one of the JAMA/Archives journals.

Biomarkers such as changes in brain volume or in cerebrospinal fluid levels of some proteins have helped scientists learn about how Alzheimer's disease develops and whether treatments for it are effective, according to background information in the article. Behavioral markers such as cognitive changes, genetic risk factors and demographic variables also seem to be associated with the condition. However, the authors write, "despite formidable evidence for the predictive validity of individual biomarkers and behavioral markers, they have rarely been examined in combined models."

Jesus J. Gomar, Ph.D., from the Benito Menni Complex Assistencial en Salut Mental, Barcelona, Spain, and colleagues sought to determine how well different classes of biomarkers and cognitive markers could predict whether patients with MCI would develop Alzheimer's disease. They also wanted to assess whether any of these factors was associated with a disproportionate magnitude of decline. The longitudinal study used information from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The study included 116 participants with MCI that converted to Alzheimer's disease in two years, 204 participants with MCI that did not convert to Alzheimer's disease and 197 cognitively healthy participants as controls.

The researchers used a variety of neuropsychological tests to assess participants' cognition and ability to function. They obtained cerebrospinal fluid samples when the study began and at annual visits for two years. At the beginning of the study, participants gave a blood sample which was examined for the presence of genes associated with Alzheimer's disease. The researchers also obtained information about participants' brain volume and cortical thickness from magnetic resonance imaging results included in the ADNI.

Analysis of the variables showed that two measures of delayed memory, as well as the cortical thickness of the left middle temporal lobe in the brain, were associated with a higher chance of converting from MCI to Alzheimer's disease at two years. A change in participants' scores on a measure of functional activities appeared to show a larger rate of decline than did changes in biomarkers. In particular, a decline in scores on the Functional Assessment Questionnaire and the Trail Making Test, part B, appeared to predict whether an individual with MCI would develop Alzheimer's disease within one year.

"Cognitive markers at baseline were more robust predictors of conversion than most biomarkers," write the authors. "Longitudinal analyses suggested that conversion appeared to be driven less by changes in the neurobiologic trajectory of the disease than by a sharp decline in functional ability and, to a lesser extent, by declines in executive function." The researchers add that in clinical practice and in clinical trials, the optimal way to accurately predict conversion to Alzheimer's disease is to use all available data.

Journal Reference:

1. J. J. Gomar, M. T. Bobes-Bascaran, C. Conejero-Goldberg, P. Davies, T. E. Goldberg. Utility of Combinations of Biomarkers, Cognitive Markers, and Risk Factors to Predict Conversion From Mild Cognitive Impairment to Alzheimer Disease in Patients in the Alzheimer's Disease Neuroimaging Initiative. Archives of General Psychiatry, 2011; 68 (9): 961 DOI: 10.1001/archgenpsychiatry.2011.96

Courtesy: ScienceDaily