DNA Packaging Discovery Reveals Principles by Which CRC Mutations May Cause Cancer (Eagle Group- Nov 18, 2012)

Fundamental understanding about how DNA works will produce a "180-degree change in focus" for researchers who study how gene packaging regulates gene activity, including genes that cause cancer and other diseases.

The discovery, by Bradley R. Cairns, PhD, Senior Director of Basic Science at HCI and a professor in the Department of Oncological Sciences, is reported in this week's online issue of the journal Nature.

Cairns's research focuses on chromatin remodeling complexes (CRCs), which are cellular protein complexes that behave like motors, expanding or compacting different portions of DNA to either express or silence genes, respectively. Before, scientists thought that the motor within CRCs waits at rest until it receives instructions. Cairns and co-author Cedric R. Clapier show that the motor within a key CRC responsible for gene packaging and assembly is intrinsically turned on, and instead requires specific instructions to turn it off.

"Many articles in the research literature show that CRCs are mutated in cancer cells. They are intimately involved in regulating gene expression -- responsible for correctly packaging genes that control growth proliferation and for unpackaging tumor suppressors," said Cairns. "This research reveals principles by which CRC mutations could cause cancer."

Chromosomes are made of long DNA strands compressed around nodes of protein called nucleosomes; when DNA is compressed, the genes in that area are turned off. Some CRCs, called disassembly CRCs, act as motors that unwind sections of DNA chains, making genes active for a given cell process. Another type, called assembly CRCs, rewinds the DNA chain, recompressing it when the process is complete. The unwind-rewind cycle is repeated continuously throughout a cell's life.

In this study, Cairns and Clapier focused on assembly CRCs. "Before this research, we thought that the motor was off unless a protein coming from another part of the cell turned it on," said Cairns. "Researchers have been searching for the switch by looking at the CRC motor to see what binds to it.

"As it turns out, we discovered that the CRC motor already carries on its flank a 'switch' that inhibits its action until a marker sequence, located on the nucleosome, is encountered. The marker flips the inhibitor switch and allows the CRC to crank the DNA chain back around the nucleosome, promoting gene packaging and silencing" Cairns said. "Our results change where future researchers should be looking to understand how CRCs are regulated -- not at the CRC motor itself, but at the 'switches' that flank the motor."

The study also describes a measuring function on the CRC that checks for the correct distance between one nucleosome and the next, telling the motor to switch off at the proper time, a function needed for gene silencing.

Cairns's lab will now examine this same switching concept in disassembly remodelers. "There are additional remodeler families with alternative functions, like DNA repair," said Cairns. "We think this concept will apply to them as well."

This research was supported by funding from the National Institutes of Health (GM60415 and CA042014) and from the Howard Hughes Medical Institute.

Journal Reference:

1.      Cedric R. Clapier, Bradley R. Cairns. Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature, 2012; DOI: 10.1038/nature11625

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The above story is reprinted from materials provided by University of Utah Health Sciences.
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New Way for Antibiotic Resistance to Spread (Eagle Group- Nov 18, 2012)

Washington State University researchers have found an unlikely recipe for antibiotic resistant bacteria.

"I was surprised at how well this works, but it was not a surprise that it could be happening," says Doug Call, a molecular epidemiologist in WSU's Paul G. Allen School for Global Animal Health. Call led the research with an immunology and infectious disease Ph.D. student, Murugan Subbiah, now a post-doctoral researcher at Texas A & M. Their study appears in a recent issue of the online journal PLOS ONE.

While antibiotics have dramatically reduced infections in the past 70 years, their widespread and often indiscriminate use has led to the natural selection of drug-resistant microbes. People infected with the organisms have a harder time getting well, with longer hospital stays and a greater likelihood of death.

Animals are a major source of resistant bugs, receiving the bulk of antibiotics sold in the U.S.

The scientists focused on the antibiotic ceftiofur, a cephalosporin believed to be helping drive the proliferation of resistance in bacteria like Salmonella and E. coli. Ceftiofur has little impact on gut bacteria, says Call.

"Given that about 70 percent of the drug is excreted in the urine, this was about the only pathway through which it could exert such a large effect on bacterial populations that can reside in both the gut and the environment," he says.

Until now, conventional thinking held that antibiotic resistance is developed inside the animal, Call says.

"If our work turns out to be broadly applicable, it means that selection for resistance to important drugs like ceftiofur occurs mostly outside of the animals," he says. "This in turn means that it may be possible to develop engineered solutions to interrupt this process. In doing so we would limit the likelihood that antibiotic resistant bacteria will get back to the animals and thereby have a new approach to preserve the utility of these important drugs."

One possible solution would be to find a way to isolate and dispose of residual antibiotic after it is excreted from an animal but before it interacts with soil bacteria.

The WSU experiments were performed in labs using materials from dairy calves. Researchers must now see if the same phenomenon takes place in actual food-animal production systems.

Funding for the study included grants from the National Institutes of Health, the WSU College of Veterinary Medicine's Agricultural Animal Health Program, the WSU Agricultural Research Center, and Call's Caroline Engle professorship in research on infectious diseases.

Other researchers were Devandra Shah and Tom Besser, both in WSU's Department of Veterinary Microbiology and Pathology and the Allen School, and Jeffrey Ullman at the University of Florida in Gainesville.

Journal Reference:

1.      Murugan Subbiah, Devendra H. Shah, Thomas E. Besser, Jeffrey L. Ullman, Douglas R. Call. Urine from Treated Cattle Drives Selection for Cephalosporin Resistant Escherichia coli in Soil. PLoS ONE, 2012; 7 (11): e48919 DOI: 10.1371/journal.pone.0048919

 

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The above story is reprinted from materials provided by Washington State University. The original article was written by Eric Sorensen.
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New Tools Developed to Better Treat ADHD Patients in Early Stages (Eagle Group- Nov 17, 2012)

Mayo Clinic researchers are presenting new findings on the early treatment of child and adolescent attention deficit hyperactivity disorder this week at the American Academy of Childhood and Adolescent Psychiatry annual meeting in San Francisco. Find out…..

In the first study, Mayo Clinic researchers required parents and teachers of children coming in for their first ADHD consultation, defined by some combination of problems such as difficulty sustaining attention, hyperactivity and impulsive behavior, consultations to complete extensive background forms and analysis. By offering incentives and stressing the importance of being prepared for the first consultation, clinicians were able to boost parent and teacher compliance from 25 to 90 percent at the Mayo Clinic Child and Adolescent ADHD Clinic. As a result, researchers have been able to better recommend treatment and therapy right off the bat.

"I'd compare treating a child with ADHD for the first time to consulting with someone who has type II diabetes -- we need to measure a diabetic patient's blood sugar level before we can properly treat them," says study lead author Jyoti Bhagia, M.D., a Mayo Clinic psychiatrist. "The same goes for ADHD. The more we know about children in the early stages of treatment, the more quickly we can get them the help they need."

In the second study, Mayo Clinic researchers gave 75 patients with ADHD at the Mayo Clinic Child and Adolescent ADHD Clinic a written, subjective evaluation to test for oppositional defiance disorder, a persistent pattern of tantrums, arguing, and angry or disruptive behavior toward authority figures.

They found that the test was far better able to pick up whether the child had the disorder than an anecdotal physician diagnosis. Of the 75 patients in the study, 27 percent, or less than a third, were diagnosed with oppositional defiance disorder by their providers. After taking the subjective test, 48 percent tested positive for oppositional defiance disorder. That shows the presence of oppositional defiance disorder with ADHD is underdiagnosed and children may not be receiving the behavioral treatment they need.

Children who have both ADHD and oppositional defiance disorder benefit from a combination of medication and behavioral therapy, says Dr. Bhagia.

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The above story is reprinted from materials provided by Mayo Clinic.

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Enhancing Breast Cancer Detection: Computer Algorithm Analyzes Thermal Images of Breasts (Eagle Group- Nov 17, 2012)

Straightforward imaging with an infrared, thermal, camera for detecting breast cancer early without the discomfort or inconvenience of mammography or biomolecular tests.

Tiago Borchartt of the Federal Fluminense University in Brazil and colleagues explain how breast thermography has up to now achieved an average sensitivity and specificity or approximately 90 percent for the detection of malignant tissue. The advantages of the technique are that it is painless, requires no contact between patient and instrumentation and is entirely non-invasive. However, a 90 percent accuracy rate implies that there is a lot of room for improvement before such a technique could become a mainstream clinical diagnostic for the early stages of breast cancer.

The team has developed new software that allows them to acquire thermal images into a computer database and so be used to help with diagnosis after the automatic extraction of the regions of interest. The same tool combines storage with feature extraction and recognition. The approach can detect the presence of problems using symmetric analysis and numerical simulations using finite element analyses allows it to analyze the relationships between internal temperature and the temperature on the breast surface during image acquisition.

So far, the researchers have tested their approach on a limited number of thermal images from 28 patients: four healthy patients, eight with cysts, eleven patients with fibroadenoma and five with carcinoma. They were able to improve the accuracy of breast thermography using their approach to 96%. The next step will be to test this in larger group of at least 2000 patients. That future project has already been approved by the ethical committee of the University Hospital of UFF.

Journal Reference:

Tiago B. Borchartt; Roger Resmini; Leonardo S. Motta; Esteban W.G. Clua; Aura Conci; Mariana J.A. Viana; Ladjane C. Santos; Rita C.F. Lima; Angel Sanchez.Combining approaches for early diagnosis of breast diseases using thermal imaging. International Journal of Innovative Computing and Applications, 2012; 4 (3/4) [link]

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The above story is reprinted from materials provided by Inderscience Publishers, via EurekAlert!, a service of AAAS.

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Hepatitis C Treatment's Side Effects Can Now Be Studied in the Lab (Eagle Group- Nov 17, 2012)

Study the new method which helps to understand failures of hepatitis C antiviral drug (in clinical trials) and also help in identifying the medication that eliminates all adverse effects, thanks to a research team led by Craig Cameron, the Paul Berg Professor of Biochemistry and Molecular Biology at Penn State University. 

The team's findings, published in the current issue of the journal PLOS Pathogens, may help pave the way toward the development of safer and more-effective treatments for hepatitis C, as well as other pathogens such as SARS and West Nile virus.

First author Jamie Arnold, a research associate in Cameron's lab at Penn State, explained that the hepatitis C virus (HCV), which affects over 170,000,000 people worldwide, is the leading cause of liver disease and, although antiviral treatments are effective in many patients, they cause serious side effects in others. "Many antiviral medications for treating HCV are chemical analogs for the building blocks of RNA that are used to assemble new copies of the virus's genome, enabling it to replicate," he said. "These medications are close enough to the virus's natural building blocks that they get incorporated into the virus's genome. But they also are different in ways that lead to the virus's incomplete replication. The problem, however, is that the medication not only mimics the virus's genetic material, but also the genetic material of the patient. So, while the drug causes damage to the virus, it also may affect the patient's own healthy tissues."

A method to reveal these adverse side effects in the safety of a laboratory setting, rather than in clinical trials where patients may be placed at risk, has been developed by the research team, which includes Cameron; Arnold; Suresh Sharma, a research associate in Cameron's lab; other scientists at Penn State; and researchers from other academic, government, and corporate labs. "We have taken anti-HCV medications and, in Petri dishes and test tubes, we have shown that these drugs affect functions within a cell's mitochondria," Cameron explained. "The cellular mitochondria -- a tiny structure known as 'the powerhouse of the cell' that is responsible for making energy known as ATP -- is affected by these compounds and is likely a major reason why we see adverse effects." Cameron noted that scientists have known for some time that certain individuals have "sick" mitochondria. Such individuals are likely more sensitive to the mitochondrial side effects of antiviral drugs.

"We know that antiviral drugs, including the ones used to treat HCV, affect even normal, healthy mitochondria by slowing ATP output," Arnold added. "While a person with normal mitochondria will experience some ATP and mitochondrial effects, a person who is already predisposed to mitochondrial dysfunction will be pushed over the 'not enough cellular energy' threshold by the antiviral drug. The person's mitochondria simply won't be able to keep up."

One of the problems with clinical trials, Arnold explained, is that a drug may be shown to be quite effective but, if even a miniscule percentage of patients have side effects, the U.S. Food and Drug Administration is obligated to put the trial on hold or stop the trial altogether. This possibility makes drug companies reluctant to invest money in drug trials after an adverse event has been observed, even when the drugs could still help millions of people. The researchers hope that their methods eventually will become a part of the pre-clinical development process for this class of antiviral drugs. "If we can show, in the lab, that a drug will cause side effects, then these compounds will not enter lengthy, expensive clinical trials and cause harm to patients " he said. "What's more, a drug company can invest its money more wisely and carefully in drug research that will produce safe and effective products. Better and more-willing investments by drug companies ultimately will help patients, because resources will be spent developing drugs that not only work, but that are safe for all patients."

Cameron added that the next step for his team is to identify the genes that make some individuals respond poorly to these particular antiviral treatments. "By taking blood samples from various patients and using the new method to test for toxicity in the different samples, we hope to discover which individuals will respond well and which will experience mitochondrial reactions, based on their genetic profiles," he said. "That is, we hope to use this method as a step toward truly personalized medicine, opening the door to pre-screening of patients so that those with mitochondrial diseases can be treated with different regimens from the start."

The team members also hope their method will be a means to study toxicity and side effects in other diseases. "Specifically, our technology will illuminate toxicity of a particular class of compounds that interrupts viral RNA synthesis," Cameron said. "While this class of compounds currently is being developed for treatment of HCV, a wide range of other RNA viruses, including West Nile virus, Dengue virus, SARS coronavirus, and perhaps even the Ebola virus, could be treated using this class of compounds as well."

In addition to Cameron, Arnold, and Sharma, other researchers who contributed to this study include Eric D. Smidansky from Penn State; Joy Y. Feng, Adrian S. Ray, Aesop Cho, Jason Perry, Jennifer E. Vela, Yeojin Park, Yili Xu, Yang Tian, Darius Babusis, Ona Barauskus, and Weidong Zhong from Gilead Sciences, Inc.; Maria L. Kireeva and Mikhail Kashlev from the Frederick National Laboratory for Cancer Research; Blake R. Peterson from the University of Kansas; and Averell Gnatt from the University of Maryland School of Medicine.

The research was funded by the National Institutes of Health and a Penn State Paul Berg Endowment.

Journal Reference:

1.      Jamie J. Arnold, Suresh D. Sharma, Joy Y. Feng, Adrian S. Ray, Eric D. Smidansky, Maria L. Kireeva, Aesop Cho, Jason Perry, Jennifer E. Vela, Yeojin Park, Yili Xu, Yang Tian, Darius Babusis, Ona Barauskus, Blake R. Peterson, Averell Gnatt, Mikhail Kashlev, Weidong Zhong, Craig E. Cameron. Sensitivity of Mitochondrial Transcription and Resistance of RNA Polymerase II Dependent Nuclear Transcription to Antiviral Ribonucleosides. PLoS Pathogens, 2012; 8 (11): e1003030 DOI:10.1371/journal.ppat.1003030

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The above story is reprinted from materials provided by Penn State. The original article was written by Katrina Voss.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.
Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of Eagle Group or its staff.

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Location, Location, Location: Membrane 'Residence' Gives Proteases Novel Abilities (Eagle Group- Nov 17, 2012)

A new mode of action for enzymes immersed in cellular membranes: How and What…??

In a report published online Nov. 13 in the new journal eLife, the Johns Hopkins scientists say their study results are the first to shed light on how these enzymes make use of their native environment to function. The particular "cellular scissors" that they studied, known as rhomboid proteases, are unusual among proteases because they cut their target proteins from inside cellular membranes. And because these and other membrane proteases have roles to play in everything from malaria to Parkinson's disease, uncovering their "inside" work could have profound implications for human health, the scientists note.

"The evolution of these proteases, which are found in all types of living organisms, gave cells a whole new set of tools for regulating biology," says principal investigator Sinisa Urban, Ph.D., associate professor of molecular biology and genetics at the Institute for Basic Biomedical Sciences at Johns Hopkins.

Proteases cut proteins for many reasons. The stomach relies on them to indiscriminately break down and digest various proteins people eat. Other proteases are more specialized and help regulate the immune system, for example. Each of these specialized proteases recognizes only specific protein "clients" and only cuts its clients at one specific site.

"Until we did this work, it was thought that specialized proteases decided which proteins to cut based on the presence or absence of a specific sequence of amino acids they recognized," says Urban. "But while most proteases work in watery environments, rhomboid proteases work in oily membranes. Their unique environment suggested to us that they may also have unique properties within the cell."

Urban notes that rhomboid proteases are like barrels with a gate that only allows certain proteins inside. Once proteins get past the gate, they interact with the "scissors" inside the barrel and get clipped and released.

For their research, Urban and his team analyzed the activity of rhomboid proteases in microscopic gel-like droplets, which are traditionally used as substitutes for cell membranes, but which are incomplete imitations. To more thoroughly assess the role of the protease's environment in its function, they also developed ways to reassemble rhomboid proteases and their clients in real cell membranes. This allowed them to use cutting-edge biophysical techniques to compare how the enzymes and clients behaved in real membranes versus membrane substitutes.

They report that rhomboid proteases allow more proteins through their gates -- and cut them at different places -- when they are in the gel than when they are in the membrane. "That told us that these proteases are less accurate in recognizing which proteins to cut in the artificial environment than in their natural one," says Urban. "The membrane clearly helps to keep the gate from swinging open and letting unnatural sites to be cut."

The researchers then took a series of different proteins and changed their makeups in a variety of ways to see which ones the rhomboid proteases could cut in living cells. By analyzing dozens of individual changes to various proteins, they found that specific sequences were not the main thing that determined which proteins were cut. Instead, the key factor was whether the protein target was unstable in a watery environment.

Urban explains that when a protein contains a segment that crosses the viscous, oily cell membrane, that segment takes on a curly cue shape, like a slinky, even if it's floppy and shapeless outside the membrane in a watery environment. "Rhomboid proteases have watery inner chambers. If the slinky shape falls apart inside, the protein gets cut. If the slinky shape remains intact, it doesn't get cut."

This insight, says Urban, opens possibilities for better understanding several diseases and ultimately for developing treatments. For example, he says, the protein that builds up in the brain of Alzheimer's patients is a target for another type of membrane-resident protease that isn't well understood either.

Co-authors of the report are Syed Moin and Sinisa Urban from the Johns Hopkins University School of Medicine and the Howard Hughes Medical Institute.

The research was supported by grants from the National Institute of Allergy and Infectious Diseases (AI066025) and the Howard Hughes Medical Institute.

Journal Reference:

1.      Syed M Moin, Sinisa Urban. Membrane immersion allows rhomboid proteases to achieve specificity by reading transmembrane segment dynamics. eLife, 2012; 1 DOI: 10.7554/eLife.00173

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The above story is reprinted from materials provided by Johns Hopkins Medicine.

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Clues to Cause of Kids' Brain Tumors (Eagle Group- Nov 17, 2012)

Insights from a genetic condition that causes brain cancer are helping scientists better understand the most common type of brain tumor in children.

  

In new research, scientists at Washington University School of Medicine in St. Louis have identified a cell growth pathway that is unusually active in pediatric brain tumors known as gliomas. They previously identified the same growth pathway as a critical contributor to brain tumor formation and growth in neurofibromatosis-1 (NF1), an inherited cancer predisposition syndrome.

"This suggests that the tools we've been developing to diagnose and treat NF1 may also be helpful for sporadic brain tumors," says senior author David H. Gutmann, MD, PhD, the Donald O. Schnuck Family Professor of Neurology.

The findings appear Dec. 1 in Genes and Development.

NF1 is among the most common tumor predisposition syndromes, but it accounts for only about 15 percent of pediatric low-grade gliomas known as pilocytic astrocytomas. The majority of these brain tumors occur sporadically in people without NF1.

Earlier research showed that most sporadic pilocytic astrocytomas possess an abnormal form of a signaling protein known as BRAF. In tumor cells, a piece of another protein is erroneously fused to the business end of BRAF.

Scientists suspected that the odd protein fusion spurred cells to grow and divide more often, leading to tumors. However, when they gave mice the same aberrant form of BRAF, they observed a variety of results. Sometimes gliomas formed, but in other cases, there was no discernible effect or a brief period of increased growth and cell division. In other studies, the cells grew old and died prematurely.

Gutmann, director of the Washington University Neurofibromatosis Center, previously showed that mouse NF1-associated gliomas arise from certain brain cells.

According to Gutmann, the impact of abnormal NF1 gene function on particular cell types helps explain why gliomas are most often found in the optic nerves and brainstem of children with NF1 -- these areas are where the susceptible cell types reside.

With that in mind, Gutmann and his colleagues tested the effects of the unusual fusion BRAF protein in neural stem cells from the cerebellum, where sporadic pilocytic astrocytomas often form, and in cells from the cortex, where the tumors almost never develop.

"Abnormal BRAF only results in increased growth when it is placed in neural stem cells from the cerebellum, but not the cortex," Gutmann says. "We also found that putting fusion BRAF into mature glial cells from the cerebellum had no effect."

When fusion BRAF causes increased cell proliferation, postdoctoral fellows Aparna Kaul, PhD and Yi-Hsien Chen, PhD, showed that it activates the same cellular growth pathway, called mammalian target of rapamycin (mTOR), that is normally also controlled by the NF1 protein. An extensive body of research into the mTOR pathway already exists, including potential treatments to suppress its function in other forms of cancer.

"We may be able to leverage these insights and our previous work in NF1 to improve the treatment of these common pediatric brain tumors, and that's very exciting," Gutmann says.

Gutmann and his colleagues are now working to identify more of the factors that make particular brain cells vulnerable to the tumor-promoting effects of the NF1 gene mutation and fusion BRAF. They are also developing animal models of sporadic pilocytic astrocytoma for drug discovery and testing.

 Journal Reference:

1.      Kaul A, Chen Y-H, Emnett RJ, Dahiya S, Gutmann DH.Pediatric glioma-associated KIAA1549:BRAF expression regulates neuroglial cell growth in a cell type-specific and mTOR-dependent manner.. Genes & Development, Dec. 1, 2012

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The above story is reprinted from materials provided by Washington University School of Medicine. The original article was written by Michael C. Purdy.

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

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

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