Integrated DNA Technologies (IDT) and Ubiquitome announced in early December 2014 a partnership to develop the Ubiquitome Freedom4 Real-Time RT-PCR Ebola Virus Assay for easy use in the field. This rapid test is designed to be run on Ubiquitome’s hand-held, battery powered real-time PCR device, the Freedom4. IDT, a market leader in the manufacture of GMP quality products for use in molecular diagnostic tests, is leveraging its PrimeTime qPCR Assay platform to develop an assay that will provide accurate and consistent test results for Ebola virus disease. Fitting in the palm of a hand, Ubiquitome’s Freedom4 instrument operates on battery power alone for up to six hours and delivers gold-standard real-time PCR performance wherever needed. The platform runs using an iPhone or laptop computer, is housed in a rugged aluminum casing and features a solid state design that includes laser-based optical detection, which is widely recognized as offering the highest performance in real-time PCR. Paul Pickering, Ubiquitome CEO, said “The Ubiquitome Freedom4 Real-Time RT-PCR Ebola Virus Assay, run on the Freedom4, will allow rapid, accurate field testing of Ebola virus disease. This is important because regions affected by this disease are often far from an established laboratory.” Stephen Gunstream, Chief Commercial Officer of IDT added, “The sensitivity and specificity of our PrimeTime qPCR Assays are well established. We are excited about how effectively we can combine IDT’s assay design expertise with Ubiquitome’s Freedom4 instrument to provide a field testing service for Ebola virus disease. This test will enable early detection and help control the spread of this devastating disease.” Testing of the Ubiquitome Freedom4 Real-Time RT-PCR Ebola Virus Assay will be conducted by Battelle in Aberdeen, Maryland, USA.

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An analysis of the genomes and epigenomes of lean and obese mice and humans has turned up a wealth of clues about how genes and the environment conspire to trigger diabetes, Johns Hopkins researchers say. Their findings reveal that obesity-induced changes to the epigenome — reversible chemical “tags” on DNA — are surprisingly similar in mice and humans, and might provide a new route to prevention and treatment of the disease, which affects hundreds of millions worldwide.

“It’s well known that most common diseases like diabetes result from a combination of genetic and environmental risk factors. What we haven’t been able to do is figure out how, exactly, the two are connected,” says Andrew Feinberg, M.D., M.P.H., Gilman Scholar and director of the Center for Epigenetics in the Institute for Basic Biomedical Sciences at the Johns Hopkins University School of Medicine. “This study takes a step in that direction.”

Feinberg has long studied the epigenome, which he compares to “software” that runs on DNA’s “hardware.” Epigenetic chemical tags affect whether and how much genes are used without changing the genetic code itself.

Feinberg wondered whether epigenetics might partly explain the skyrocketing worldwide incidence of type 2 diabetes. Obesity is a well-established risk factor for the disease, so Feinberg’s research group teamed with that of a group led by G. William Wong, Ph.D., an associate professor of physiology in the Center for Metabolism and Obesity Research at Johns Hopkins, to study the epigenetics of otherwise identical mice that were fed either normal or high-calorie diets.

Analyzing epigenetic marks at more than 7 million sites in the DNA of the mice’s fat cells, the researchers found clear differences between the normal and obese mice. Some sites that bore chemical tags called methyl groups in the lean mice were missing them in the obese mice, and vice versa. The methyl groups prevent genes from making proteins.

With colleagues at Sweden’s Karolinska Institutet, Feinberg and his team then tested whether the same pattern of differences held in fat cells from lean and obese people, and found, to their surprise, that it did. “Mice and humans are separated by 50 million years of evolution, so it’s interesting that obesity causes similar epigenetic changes to similar genes in both species,” Feinberg says. “It’s likely that when food supplies are highly variable, these epigenetic changes help our bodies adapt to temporary surges in calories. But if the high-calorie diet continues over the long term, the same epigenetic pattern raises the risk for disease.”

The research team also found that some of the epigenetic changes associated with obesity affect genes already known to raise diabetes risk. Others affect genes that had not been conclusively linked to the disease, but that turned out to have roles in how the body breaks down and uses nutrients, a process called metabolism. “This study yielded a list of genes that previously have not been shown to play a role in diabetes,” says Wong. “In further tests, we showed that at least some of these genes indeed regulate insulin action on sugar uptake; they offer insights into new potential targets for treating type 2 diabetes.”

In addition to providing leads for drug development, the results also suggest that an epigenetic test could be developed to identify people much earlier on the path to diabetes, giving more hope for preventing the disease, Feinberg says. John Hopkins Medicine

A new intermediate step and unexpected enzymatic activity in a metabolic pathway in the body, which could lead to new drug design for psychiatric and neurodegenerative diseases, has been discovered by researchers at Georgia State University.

The research team has been studying a metabolic pathway called the tryptophan kynurenine pathway, which is linked to psychiatric and neurodegenerative disorders, including depression, anxiety, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, AIDS dementia complex, asphyxia in newborns and epilepsy. The medical potential of this pathway warrants detailed study to provide information about the pathway’s enzymes and their regulation.

This pathway produces several neurotransmitter regulators and is responsible for metabolizing nearly 99 percent of the tryptophan in the body. Tryptophan is a precursor of serotonin, the neurotransmitter responsible for mood.

The researchers determined the structure and mechanism of an enzyme in the kynurenine pathway, AMSDH.

To better understand the rapid chemical reaction catalysed by this enzyme, Dr. Aimin Liu, professor in the Department of Chemistry and core member of the Center for Diagnostics and Therapeutics at Georgia State, organized a research team, including graduate students Lu Huo, Ian Davis, Fange Liu and Shingo Esaki, and researchers at Brookhaven National Laboratory and Kansai University in Osaka, Japan. They used new scientific techniques, including time-lapse crystallography and single-crystal spectroscopy, to slow down the reaction rate by nearly 10,000 times. This allowed them to observe a new intermediate step, the thiohemiacetal intermediate, and discover an unexpected isomerase activity in AMSDH.

‘By doing this, we find new chemistry, and we also open up avenues for others to design specific drugs to target this pathway,’ Liu said. ‘This pathway is highly associated with neurodegenerative diseases and depression.’

The researchers took a high concentration of the purified protein, grew single crystals, mixed them with their substrate and froze them at different time points in liquid nitrogen at 77 Kelvin to stop all molecular activity. They sent the crystals to Argonne National Laboratory for remote data collection. The X-ray diffraction patterns collected there were used to create an electron density map, a 3-D, atomic-level resolution of the molecule’s shape. The researchers used time-lapse crystallography and single-crystal spectroscopy to observe intermediate steps of the reaction.

‘This is the first absorbance spectrum of this intermediate,’ Davis said. ‘When we look for this in solution assays, we don’t see this absorbance band because this intermediate is very short-lived in solution. But by doing it in crystal and freezing it down, you can actually see it in the crystalline state.

‘Enzymes work by stabilizing reactive intermediates. Through this isomerization mechanism, we found a new reactive intermediate stabilized by this enzyme. So if you want to design a drug, your best bet is to try and make something that looks very similar to this so that it will bind to the enzyme. That’s a general strategy for drug design. You want to try and make drugs that look very similar to transition states. Basically, we found a new transition state in this work.’

Information from the study has been deposited in the protein database, which can be accessed by other scientists. EurekAlert

Researchers at UT Southwestern Medical Center have identified hyaluronon (HA) as a critical substance made by the body that protects against premature births caused by infection. Pre-term birth from infection is the leading cause of infant mortality in many countries according to the World Health Organization. The findings of the study are the first to identify the specific role that HA plays in the reproductive tract.

Dr. Yucel Akgul, first author and senior author Dr. Mala Mahendroo
“We found that HA is required to allow the epithelial lining of the reproductive tract to serve as the first line of defence against bacterial infections,” said senior author Dr. Mala Mahendroo, an Associate Professor in the Department of Obstetrics and Gynecology’s Cecil H. and Ida Green Center for Reproductive Biology Sciences. “Because of this action, HA offers cervical protection against the bacterial infections that cause 25 to 40 percent of pre-term births in women.”

Hyaluronon is a natural substance found in many tissues, and is both a lubricant and a beneficial component of eyes, joints, and skin. It has long been thought to play an essential role in increasing the cervix’s flexibility during the birth process; however, the study, which was conducted using mouse models, showed that HA is not essential for increased cervical pliability during late pregnancy. Rather, the substance plays an important barrier role in epithelial cells of the lower reproductive tract and in so doing protects against infection-related pre-term birth. The World Health Organization estimates that 1.09 million children under age 5 die from direct complications of being born prematurely, meaning before the 37th week of pregnancy.

Previous studies by UT Southwestern reproductive biology researchers showed that HA is present in both the cervix and cervical mucus of pregnant women. Next steps include determining the mechanism by which HA affects cervical protection against infection.

“This study demonstrates that HA plays a crucial role in the epithelial barrier as well as the cervix’s mucus,” said Dr. Yucel Akgul, first author of the study and research scientist in the Department of Obstetrics and Gynecology. “Our next step is to identify exactly how HA protects the cervix, which can have important clinical implications in the effort to reduce infection-mediated pre-term labour.” UT Southmwestern Medical Center

Genetic mutations may link smoking and alcohol consumption to destruction of the pancreas observed in chronic pancreatitis, according to a 12-year study led by researchers at the University of Pittsburgh School of Medicine. The findings provides insight into why some people develop this painful and debilitating inflammatory condition while most heavy smokers or drinkers do not appear to suffer any problems with it.

The process appears to begin with acute pancreatitis, which is the sudden onset of inflammation causing nausea, vomiting and severe pain in the upper abdomen that may radiate to the back, and is typically triggered by excessive drinking or gallbladder problems, explained senior investigator David Whitcomb, M.D., Ph.D., chief of gastroenterology, hepatology and nutrition, Pitt School of Medicine. Up to a third of those patients will have recurrent episodes of acute pancreatitis, and up to a third of that group develops chronic disease, in which the organ becomes scarred from inflammation.

“Smoking and drinking are known to be strong risk factors for chronic pancreatitis, but not everyone who smokes or drinks damages their pancreas,” Dr. Whitcomb said. “Our new study identifies gene variants that when combined with these lifestyle factors make people susceptible to chronic pancreatitis and may be useful to prevent patients from developing it.”

In the North American Pancreatitis Study II consortium, researchers evaluated gene profiles and alcohol and smoking habits of more than 1,000 people with either chronic pancreatitis or recurrent acute pancreatitis and an equivalent number of healthy volunteers. The researchers took a closer look at a gene called CTRC, which can protect pancreatic cells from injury caused by premature activation of trypsin, a digestive enzyme inside the pancreas instead of the intestine, a problem that has already been associated with pancreatitis.

They found that a certain variant of the CTRC gene, which is thought to be carried by about 10 percent of Caucasians, was a strong risk factor for alcohol- or smoking-associated chronic pancreatitis. It’s possible that the variant fails to protect the pancreas from trypsin, leaving the carrier vulnerable to ongoing pancreatic inflammation and scarring.

“This finding presents us with a window of opportunity to intervene in the diseases process,” Dr. Whitcomb said. “When people come to the hospital with acute pancreatitis, we could screen for this gene variant and do everything possible to help those who have it quit smoking and drinking alcohol, as well as test new treatments, because they have the greatest risk of progressing to end-stage chronic pancreatitis.” University of Pittsburgh Health Sciences