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Researchers report novel approach for single molecule electronic DNA sequencing

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Schematic of single molecule DNA sequencing by a nanopore with phosphate-tagged nucleotides. Each of the four nucleotides will carry a different tag. During SBS, these tags, attached via the terminal-phosphate of the nucleotide, will be released into the nanopore one at a time where they will produce unique current blockade signatures for sequence determination. A large array of such nanopores will lead to high throughput DNA sequencing.

(Phys.org)DNA sequencing is the driving force behind key discoveries in medicine and biology. For instance, the complete sequence of an individual's genome provides important markers and guidelines for medical diagnostics and healthcare. Up to now, the major roadblock has been the cost and speed of obtaining highly accurate DNA sequences. While numerous advances have been made in the last 10 years, most current high-throughput sequencing instruments depend on optical techniques for the detection of the four building blocks of DNA: A, C, G and T. To further advance the measurement capability, electronic DNA sequencing of an ensemble of DNA templates has also been developed.

Recently, it has been shown that DNA can be threaded through protein nanoscale pores under an applied electric current to produce electronic signals at single molecule level. However, because the four nucleotides are very similar in their chemical structures, they cannot easily be distinguished using this technique. Thus, the research and development of a single-molecule electronic DNA sequencing platform is the most active area of investigation and has the potential to produce a hand-held DNA sequencer capable of deciphering the genome for personalized medicine and basic biomedical research.

A team of researchers at Columbia University, headed by Dr. Jingyue Ju (the Samuel Ruben-Peter G. Viele Professor of Engineering, Professor of Chemical Engineering and Pharmacology, Director of the Center for Genome Technology and Biomolecular Engineering), with colleagues at the National Institute of Standards and Technology (NIST) led by Dr. John Kasianowicz (Fellow of the American Physical Society), have developed a novel approach to potentially sequence DNA in nanopores electronically at single molecule level with single-base resolution. This work, entitled "PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis" is now available in the open access online journal, Scientific Reports, from the Nature Publication group.

The reported nanopore-based sequencing by synthesis (Nano-SBS) strategy can accurately distinguish four DNA bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides at the single molecule level for sequence determination. The basic principle of the Nano-SBS strategy is described as follows. As each nucleotide analog is incorporated into the growing DNA strand during the polymerase reaction, its tag is released by phosphodiester bond formation. The tags will enter a nanopore in the order of their release, producing unique ionic current blockade signatures due to their distinct chemical structures, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof-of-principle, the research team attached four different length polymer tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate (a modified DNA building block) and demonstrated efficient incorporation of the nucleotide analogs during the polymerase reaction, as well as better than baseline discrimination among the four tags at single molecule level based on their nanopore ionic current blockade signatures. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

In previous work, the Center of Genome Technology & Biomolecular Engineering at Columbia University, led by Professor Ju and Dr. Nicholas J. Turro (William P. Schweitzer Professor of Chemistry), developed a four-color DNA sequencing by synthesis (SBS) platform using cleavable fluorescent nucleotide reversible terminators (NRT), which is licensed to Intelligent Bio-Systems, Inc., a QIAGEN company. SBS with cleavable fluorescent NRTs is the dominant approach used in the next generation DNA sequencing systems. Dr. Kasianowicz and his group at NIST pioneered the investigation of nanopores for single molecule analysis. They previously reported that different length polymers, polyethylene glycols (PEGs), could be distinguished by their unique effects on current readings in a -hemolysin protein nanopores at single molecule level and subsequently developed a theory for the method. Their results provide the proof-of-concept for single molecule mass spectrometry. The combination of the SBS concept with the distinct nanopore-detectable electronic tags to label DNA building blocks led to the development of the single-molecule electronic Nano-SBS approach described the current Scientific Reports article.

As lead author Dr. Shiv Kumar points out, "The novelty of our approach lies in the design and use of four differently tagged nucleotides, which upon incorporation by DNA polymerase, release four different size tags that are distinguished from each other at the single molecule level when they pass through the nanopore. This approach overcomes any constraints imposed by the small differences among the four nucleotides, a challenge which most nanopore sequencing methods have faced for decades." Moreover, the technique is quite flexible; with PEG tags as prototypes, other chemical tags can be chosen to provide optimal separation in different nanopore systems.

With further development of this Nano-SBS approach, such as the use of large arrays of protein or solid nanopores, this system has the potential to accurately sequence an entire human genome rapidly and at low cost, thereby enabling it to be used in routine medical diagnoses.

More information: Scientific Reports, 2, 684 DOI:10.1038/srep00684, 2012

Journal reference: Scientific Reports

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Researchers report novel approach for single molecule electronic DNA sequencing

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Under Controlled: Why the New GMO Panic Is More Sensational Than Sense | The Crux

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Scicurious is a PhD in Physiology, and is currently a postdoc in biomedical research. Follow on Twitter @Scicurious and read her blogs at Scientific American and at Neurotic Physiology.

A new toxicology study states that rats eating genetically modified food and the weedkiller Roundup develop huge tumors and die. But many scientists beg to differ, and a close look at the study shows why.

Genetically modified organisms (GMOs) have always been a controversial topic. On the one hand are the many benefits: the higher crop yields from pesticide- and insect-resistant crops, and the nutritional modifications that can make such a difference in malnourished populations. On the other side is the question that concerns many people: We are modifying the genes of our food, and what does that mean for our health? These are important question, but the new study claiming to answer them misses the mark. It has many horrifying pictures of rats with tumors, but without knowledge about the control rats, what do those tumors mean? Possibly, nothing at all.

The recent study, from the Journal of Food and Chemical Toxicology has fueled the worst fears of the GMO debate. The study, by Italian and French groups, evaluated groups of rats fed different concentrations of maize (corn) tolerant to Roundup or Roundup alone, over a two year period, the longest type of toxicology study. (For an example of one performed in the U.S., see here.) The group looked at the mortality rates in the aging rats, as well as the causes of death, and took multiple samples to assess kidney, liver, and hormonal function.

The presented results look like a toxicologists nightmare. The authors reported high rates of tumor development in the rats fed Roundup and the Roundup-tolerant maize. There are figures of rats with visible tumors, and graphs showing death rates that appear to begin early in the rats lifespan. The media of course picked up on it, and one site in particular has spawned some reports that sound like mass hysteria. It was the first study showing that genetically modified foods could produce tumors at all, let alone the incredibly drastic ones shown in the paper.

But can GMOs really produce such huge tumors? This paper isnt convincing. Following the release of the study, numerous scientists questioned the findings, citing anomalies throughout the paper that normally should have been corrected or resolved through the peer-review process. In particular, there are problems with the statistics performed on the data, the way the data were presented, and the numbers and types of animals used in the study.

First, the numbers. The authors examined groups of male and female rats in four different conditions: GMO food alone, GMO + Roundup, Roundup alone, and controls (normal food with no Roundup). For each experimental condition, there were three different doses of either the GMO maize (as a percent of the diet), Roundup, or both; the amount of doses of Roundup were all well below the approved doses. The 20 groups each contained 10 individuals, for a full total of 200 rats (100 male and 100 female). While 10 rats per condition might seem low, in a power analysis used to detect differences in response to, say a Roundup and non-Roundup condition, this would probably be OK. But how many final comparisons were the authors making? In the end, the authors compared each experimental condition to the same group of control rats, something that could severely bias the results. In most well-performed experiments, there would be a separate group of control rats for each condition, the GMO food alone, the GMO + Roundup, and the Roundup alone. The controls used for the study, as Anthony Trewavas, a cell biologist at the University of Edinburgh, pointed out in a press release response, are inadequate to make any deduction.

Then of course, there is the question of the animals themselves. Who were these rats? As it turns out, the rats used in the study were the Sprague Dawley rat strain, a widely used strain in biomedical and behavioral research. Unfortunately, this strain is prone to specific diseasesincluding the development of tumors. Up to 57% of female Sprague Dawley rats have been shown in other studies to develop tumors, especially mammary tumors, spontaneously. Males develop tumors at fairly high incidence as well. But in their striking mortality numbers for the study, showing the type and incidence of tumor development, the authors of the study do not show any of the control groups, and so we cannot actually compare the death rates of any of the GMO and Roundup exposures to controls. Tom Sanders, head of the Nutritional Sciences Research Division at Kings College London, pointed this fact out in the press-release response. Most toxicology studies are terminated at normal lifespan i.e. 2 years. Immortality is not an alternative. A careful read of the findings shows that the control group suffered a spontaneous death rate of 30% for males and 20% for females. But the authors do not state what caused the death. Did the dead animals develop tumors? Did control animals that survived develop tumors? We dont know. The authors did not show us.

Not only do they not show us, they do not present statistics to tell us the full story. In comparison to the 50% male death rate for the GMO maize dietis a 30% death rate in controls any better? There are no statistical analyses of how death rates compare between the different treatment groups and controls, only percentages. The way the data were analyzed is also unusual and highly complicated. This struck many of the scientists who read the study (including me) as odd. When comparing groups of doses as these authors did, there are simple enough statistical tests that will easily differentiate among the groups. Why were these tests not used? Why were the authors required to develop a highly convoluted analysis for something as simple as mortality rate?

In the end, while the results of the study look very drastic, there are too many issues to conclude that GMO maize and Roundup cause tumor formation. All we can really conclude is that rats who are prone to develop tumorsdevelop tumors, whether they are fed GMO maize, Roundup, both, or neither. In addition to the problems with the paper itself, the results contradicts a large amount of literature showing now difference in health consequences following consumption of GMOs. The potential health consequences of roundup exposure and GMOs should be carefully studied and evaluated, but studies like this one do not provide the answers, and only add to the hype.

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Under Controlled: Why the New GMO Panic Is More Sensational Than Sense | The Crux

New science course to be offered on OU’s Arezzo campus

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New science course to be offered on Italian campus

Microbiology classes offered at OU in Arezzo, July 2013

Basic Immunology: A 4000-level course that teaches students about the bodys immune response when it encounters pathogens. It will also show how the immune system develops and how it can make mistakes and cause autoimmunity, allergies and cancer.

Pathogenic Microbiology: A 4000-level course that teaches students about pathogens that try to cause infections. It also will talk about emerging pathogens effects on society, as well as health care services.

A new microbiology study abroad program will infect OUs Arezzo campus next July and make it easier for science majors to earn credit while abroad.

The summer program will include OUs basic immunology and pathogenic microbiology courses and will join two other science programs already offered in Arezzo Organic Chemistry/Chemistry & Wine Culture and Chemistry & Art.

Science classes offered abroad are a rare phenomena for a number of reasons, immunology professor Casie Collamore said in an email.

I think part of the rarity is because it seems daunting to offer hard science courses in a four week time frame, she said. Some subjects just cant be tailored to fit such a tight schedule and expect the students to really absorb the material. Another problem is that many hard science faculty also have research labs that require their attention, and it is difficult to leave the lab bench and their students for a long period of time.

This isnt the first time the microbiology department has attempted to offer classes abroad, Collamore said. A few years ago, pathogenic microbiology professor Tyrrell Conway submitted a proposal to teach a microbiology class, but it was denied because it wasnt going to be taught alongside a second course.

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New science course to be offered on OU's Arezzo campus

Columbia researchers report novel approach for single molecule electronic DNA sequencing

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Public release date: 21-Sep-2012 [ | E-mail | Share ]

Contact: Beth Kwon beth.kwon@columbia.edu 212-854-6581 Columbia University

DNA sequencing is the driving force behind key discoveries in medicine and biology. For instance, the complete sequence of an individual's genome provides important markers and guidelines for medical diagnostics and healthcare. Up to now, the major roadblock has been the cost and speed of obtaining highly accurate DNA sequences. While numerous advances have been made in the last 10 years, most current high-throughput sequencing instruments depend on optical techniques for the detection of the four building blocks of DNA: A, C, G and T. To further advance the measurement capability, electronic DNA sequencing of an ensemble of DNA templates has also been developed. Recently, it has been shown that DNA can be threaded through protein nanoscale pores under an applied electric current to produce electronic signals at single molecule level. However, because the four nucleotides are very similar in their chemical structures, they cannot easily be distinguished using this technique. Thus, the research and development of a single-molecule electronic DNA sequencing platform is the most active area of investigation and has the potential to produce a hand-held DNA sequencer capable of deciphering the genome for personalized medicine and basic biomedical research.

A team of researchers at Columbia University, headed by Dr. Jingyue Ju (the Samuel Ruben-Peter G. Viele Professor of Engineering, Professor of Chemical Engineering and Pharmacology, Director of the Center for Genome Technology and Biomolecular Engineering), with colleagues at the National Institute of Standards and Technology (NIST) led by Dr. John Kasianowicz (Fellow of the American Physical Society), have developed a novel approach to potentially sequence DNA in nanopores electronically at single molecule level with single-base resolution. This work, entitled "PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis" is now available in the open access online journal, Scientific Reports (2, 684 DOI:10.1038/srep00684, 2012), from the Nature Publication group.

The reported nanopore-based sequencing by synthesis (Nano-SBS) strategy can accurately distinguish four DNA bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides at the single molecule level for sequence determination. The basic principle of the Nano-SBS strategy is described as follows. As each nucleotide analog is incorporated into the growing DNA strand during the polymerase reaction, its tag is released by phosphodiester bond formation. The tags will enter a nanopore in the order of their release, producing unique ionic current blockade signatures due to their distinct chemical structures, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof-of-principle, the research team attached four different length polymer tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate (a modified DNA building block) and demonstrated efficient incorporation of the nucleotide analogs during the polymerase reaction, as well as better than baseline discrimination among the four tags at single molecule level based on their nanopore ionic current blockade signatures. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

In previous work, the Center of Genome Technology & Biomolecular Engineering at Columbia University, led by Professor Ju and Dr. Nicholas J. Turro (William P. Schweitzer Professor of Chemistry), developed a four-color DNA sequencing by synthesis (SBS) platform using cleavable fluorescent nucleotide reversible terminators (NRT), which is licensed to Intelligent Bio-Systems, Inc., a QIAGEN company. SBS with cleavable fluorescent NRTs is the dominant approach used in the next generation DNA sequencing systems. Dr. Kasianowicz and his group at NIST pioneered the investigation of nanopores for single molecule analysis. They previously reported that different length polymers, polyethylene glycols (PEGs), could be distinguished by their unique effects on current readings in a -hemolysin protein nanopores at single molecule level and subsequently developed a theory for the method. Their results provide the proof-of-concept for single molecule mass spectrometry. The combination of the SBS concept with the distinct nanopore-detectable electronic tags to label DNA building blocks led to the development of the single-molecule electronic Nano-SBS approach described the current Scientific Reports article (09/21/2012).

As lead author Dr. Shiv Kumar points out, "The novelty of our approach lies in the design and use of four differently tagged nucleotides, which upon incorporation by DNA polymerase, release four different size tags that are distinguished from each other at the single molecule level when they pass through the nanopore. This approach overcomes any constraints imposed by the small differences among the four nucleotides, a challenge which most nanopore sequencing methods have faced for decades." Moreover, the technique is quite flexible; with PEG tags as prototypes, other chemical tags can be chosen to provide optimal separation in different nanopore systems.

With further development of this Nano-SBS approach, such as the use of large arrays of protein or solid nanopores, this system has the potential to accurately sequence an entire human genome rapidly and at low cost, thereby enabling it to be used in routine medical diagnoses.

###

The authors of the Scientific Reports article were Shiv Kumar, Chuanjuan Tao, Minchen Chien, Brittney Hellner, Arvind Balijepalli, Joseph W.F. Robertson, Zengmin Li, James J. Russo, Joseph E. Reiner, John J. Kasianowicz, and Jingyue Ju. The study was supported by a grant from the National Institutes of Health, a National Research Council/NIST/NIH Research Fellowship, and a grant from the NIST Office of Law Enforcement Standards.

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Columbia researchers report novel approach for single molecule electronic DNA sequencing

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DNA helps Wyckoff police nab 'motorcycle burglar'

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WYCKOFF Police arrested a man known they called the "motorcycle burglar" this morning after matching him to DNA found at one of his victim's homes.

According to Wyckoff Chief Benjamin Fox, officers responded to a Nancy Lane residence in July 2011 after a homeowner reported that approximately $3,000 worth of jewelry had gone missing from her home.

A neighbor had observed a man activating an alarm system as he fled the home, and the man rode past the homeowner on a motorcycle as she was arriving home.

During an investigation, police found droplets of blood inside the home, along with a crowbar and a pair of latex gloves that had been discarded as the man rode away on the motorcycle, Fox said. They then matched DNA samples from the blood and gloves to 51-year-old Lee Malsch of Paterson, whose extensive criminal history included past burglaries.

Police obtained a warrant for Malsch's arrest on Sept. 11, but had trouble locating him. With the help of the Passaic County Sheriff's Department, however, they were able to find him this morning and take him into custody.

He was charged with burglary and theft, and is currently awaiting a bail hearing at the Bergen County Jail in Hackensack.

Fox praised the work of the investigating officers, saying that burglaries can often be difficult to solve.

"My guys don't solve every crime. No department does. But when they have evidence to works ith, they do everything that they can to apprehend those responsible," he said. "That's what they did here, and this community should be grateful."

Police were unable to recover any of the jewelry stolen from the home in 2011.

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DNA helps Wyckoff police nab 'motorcycle burglar'

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Rice to launch new doctoral program in systems, synthetic and physical biology

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Starting in the fall of 2013, Rice will offer a new doctoral program in systems, synthetic and physical biology that was officially approved by the Rice Senate on Sept. 12. The program was originally envisioned by assistant professor of bioengineering Oleg Igoshin, professor of statistics Marek Kimmel, professor of biochemistry and cell biology Yousif Shamoo, and other professors from the Wiess School of Natural Sciences and the George R. Brown School of Engineering.

With foundations in quantitative and life sciences, the program aims to make important advances in bioscience with work from students and 34 faculty members who specialize in biology, chemistry, computer science, engineering, mathematics, statistics or physics. An additional goal is to expand research, according to Igoshin.

Another goal of the program is to enable us to do research we couldnt do before, SSPB Director Michael Deem said. We will have more students to work with, and we hope to attract additional funding from the federal government or from private foundations.

This program is the first of its kind in the United States, Igoshin said.

This is the first program in the country that has synthetic biology in its name, and this name is very much related to its foundation, Igoshin said. We see this new biology as a system: a whole with interacting parts.

The program will feature one core course open for undergraduate enrollment but will otherwise be exclusively open to graduate students. It will be highly selective because the faculty are looking to recruit eight first-year graduate students per year, Deem said.

According to Igoshin, the program will be highly interdisciplinary and will include faculty members from eight departments in the schools of engineering and natural sciences.

We observed [that] the large expansion of Rice faculty [who were] doing biology-related research were not necessarily from the biology department, but from computer science, statistics, biological and chemical engineering, Igoshin said. There was a good resource of talented people to create such a program.

According to Igoshin, this program is designed to develop a new approach toward the study of biology.

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Rice to launch new doctoral program in systems, synthetic and physical biology

Fearful Memories Can Be Permanently Erased

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September 21, 2012

redOrbit Staff & Wire Reports Your Universe Online

Emotional memories can be erased shortly after they are formed through behavioral intervention alone, without the aid of medications, according to a new study published Thursday in the journal Science.

The breakthrough offers a major step forward in understanding where fearful memories are processed in the brain, and how to permanently erase them. The research could be particularly helpful for people suffering from conditions such as anxiety and post-traumatic stress disorder, the researchers said.

When a person learns something, a lasting long-term memory is created through a process of consolidation, which is based on the formation of proteins. When we remember something, the memory becomes unstable for a short time, and is then restabilized by another consolidation process. In other words, we are not remembering what originally happened, but rather what we remembered the last time we thought about what happened.

The studys researchers sought to examine whether disrupting the reconsolidation process that follows upon remembering something could affect the content of memory.

They showed a small group of study participants a neutral picture while simultaneously administering an electric shock so that the picture came to elicit fear, triggering the formation of a fear memory.

The same picture was then shown to the participants the following day, but without an accompanying shock, in order to activate this fear memory (the beginning of the reconsolidation process).

Although seeing the picture again reactivated the original fear memory, it also, theoretically, made the memory easier to erase.

The researchers then divided the subjects into two groups. The first subgroup was repeatedly shown the picture, without the shocks, in order to disrupt their reconsolidation process so they would stop associating one with the other.

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Fearful Memories Can Be Permanently Erased

Billionaires Fund A 'Manhattan Project' For Nutrition And Obesity

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Enlarge Courtesy of the John and Laura Arnold Foundation

Billionaires John and Laura Arnold are betting that the country's top nutrition researchers can get to the bottom of the obesity epidemic.

Billionaires John and Laura Arnold are betting that the country's top nutrition researchers can get to the bottom of the obesity epidemic.

Why would a billionaire energy trader-turned-philanthropist throw his foundation's dough behind a new think tank that wants to challenge scientific assumptions about obesity?

John Arnold, 38, whose move from Enron to a spectacularly successful hedge fund got him on the list of wealthiest Americans, isn't crazy about talking to the press. But certainly his decision with his wife Laura to back a newly launched operation called the Nutrition Science Initiative, or NuSI, is an intriguing one.

Obesity, and all the dietary confusion that swirls around it, is clearly a problem that isn't going away. But NuSI says large-scale scientific studies that tackle fundamental questions like how food really affects fat, hormones and the brain are what's needed to solve it more than anything else.

We're told by NuSI's president, Peter Attia, a Stanford and Johns Hopkins-trained doctor, that Arnold's interest in the cause started with a podcast featuring science journalist and NuSI co-founder, Gary Taubes.

Taubes has been arguing for the last several years in books and articles in the New York Times Magazine that current dietary guidelines and beliefs about what has caused the obesity epidemic are wrong and based on poor science. Attia says Arnold approached Taubes after Arnold realized he could bring resources to bear on the problem $5 million in seed money to fund "good" studies that are usually prohibitively expensive.

"In ... nutrition science, the research is inadequate, so our guiding information is not based on rigorous science," Meredith Johnson, a spokeswoman for the John and Laura Arnold Foundation, told The Salt in an email.

One reason Attia agrees it's inadequate is that "it's really quite difficult to study nutrition in humans at the level of precision that scientists in other fields can get."

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Billionaires Fund A 'Manhattan Project' For Nutrition And Obesity

Wild boars are reservoir of HEV: High prevalence among forestry workers in eastern France

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Nearly one third of forestry workers in parts of eastern France are infected with Hepatitis E virus (HEV), according to a paper in the September Journal of Clinical Microbiology. Wild boars in the same region are also heavily infected. HEV is endemic in developing nations, but heretofore, HEV infection in industrialized nations has been most closely correlated with travel to developing nations.

The prevalence of HEV was found to be 14 percent among wild boar, about half that in pigs, says principal investigator Pierre Coursaget of the University of Tours, France. An earlier study found 12 percent prevalence among boar in The Netherlands. Among humans in the current study, the prevalence of anti-HEV antibodies increases with age, and varies with occupation and geographic location within eastern France. "The frequency of HEV infections in humans did not correlate with the number of pigs, locally, but there is good correlation with the number of car accidents due to wild boars," a surrogate for contact between humans and wild boars, says Coursaget.

HEV is transmitted orally and fecally, with mortality rates of 1-3 percent in the general population, rising to 20-25 percent among pregnant women. In developing countries, outbreaks appear to arise from fecally contaminated water supplies. In Japan, and in Europe, consumption of wild boar or liver is associated with a high risk of acquiring hepatitis E virus infection, according to the report. However, the fact that HEV is absent among children in France suggests that eating ham is safe. Coursaget says the immune system in healthy people generally eradicates the infection, and that it is not sexually transmitted.

Deer also are known to be infected with HEV, says Coursaget. "People in contact with HEV-infected animals or their environment must be aware of the possibility of HEV infection," he says. He is currently studying HEV infection in forestry workers, veterinarians, and pig farmers in different regions of France, in an effort to quantify risk factors. The current study also compared several antibody tests for HEV, with one, the HEV ELISA test, from MP Biologicals, proving superior to the other two.

More information: A. Carpentier, et al., 2012. High hepatitis E virus seroprevalence in forestry workers and wild boars in France. J. Clin Microbiol. 50:2888-2893. bit.ly/asmtip0912e

Journal reference: Journal of Clinical Microbiology

Provided by American Society for Microbiology

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Wild boars are reservoir of HEV: High prevalence among forestry workers in eastern France

Study abroad program gets more class options

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Study abroad program gets more class options

A new microbiology study abroad program will infect OUs Arezzo campus next July and make it easier for science majors to earn credit while abroad.

The summer program will include OUs basic immunology and pathogenic microbiology courses and will join two other science programs already offered in ArezzoOrganic Chemistry/Chemistry & Wine Culture and Chemistry & Art.

Science classes offered abroad are rare phenomena for a number of reasons, immunology professor Casie Collamore said in an email.

I think part of the rarity is because it seems daunting to offer hard science courses in a four week time frame, she said. Some subjects just cant be tailored to fit such a tight schedule and expect the students to really absorb the material. Another problem is that many hard science faculty also have research labs that require their attention, and it is difficult to leave the lab bench and their students for a long period of time.

This isnt the first time the microbiology department has attempted to offer classes abroad, Collamore said. A few years ago, pathogenic microbiology professor Tyrrell Conway submitted a proposal to teach a microbiology class, but it was denied because it wasnt going to be taught alongside a second course.

As microbiology advisor, Collamore spoke with a number of microbiology students who wanted to study abroad but couldnt because none of the offered classes were required for their degrees. When she heard that Conways proposal had been denied, she spoke with him and they came up with a new proposal together, Collamore said.

The two professors thought Arezzo would be the perfect place to teach the two classes because it was the birthplace of Francesco Redi, a physician who helped disprove spontaneous generation. This finding led to the Golden Age of Microbiology, a time during which scientists discovered that microbes exist and cause disease, Collamore said.

It is thought [Francesco Redis] body is buried there as well, but nobody can find it, Collamore said. It seemed like a very fitting place to teach the two subjects.

Conway and Collamore will teach the pathogenic microbiology course and immunology course respectively. While Pathogenic Microbiology is required for microbiology majors, Basic Immunology is a popular course commonly taken by microbiology majors to meet their elective requirements, Collamore said.

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DNA evidence links Vallejo man to January stabbing in SLO, police say

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Using DNA matches off a knife, San Luis Obispo police detectives were able to identify a suspect in an attempted murder case, and then arrested a Vallejo man for the alleged crime.

In a news release issued Thursday, police Lt. Jeff Smith said Austin Sarna, 21, was arrested Wednesday in Vallejo after the DNA evidence linked him to an attack that occurred in January.

Sarna was taken into custody without incident, and was transported to San Luis Obispo County Jail, where he remains on a no-bail warrant.

Smith said that at 12:30 a.m. on Jan. 20, police were called to the intersection of Broad and Monterey streets on the report of a man who had been stabbed and was bleeding profusely from his arm.

Police learned that several men got into an altercation with two or more others. Trevor Tice, 27, of Atascadero, was stabbed multiple times in the back and arm. Zachary Lerno, 26, was stabbed once in the head.

"During the investigation there were limited details regarding the suspect due to a lack of witnesses and levels of intoxication," Smith said. But the knife used in the attack was found by officers and taken as evidence.

The suspected weapon was sent to a state crime lab for analysis. One DNA sample matched Tice; another matched Sarna. Investigators then contacted the two male victims and witnesses, who identified Sarna as one of the men in the altercation.

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DNA evidence links Vallejo man to January stabbing in SLO, police say

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DNA barcoding can ID natural health products

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ScienceDaily (Sep. 19, 2012) DNA barcoding developed by University of Guelph researchers has proven up to 88 per cent effective in authenticating natural health products, according to a new U of G study.

The study appears in the latest issue of Food Research International. It's a crucial finding because the health product industry is under-regulated worldwide and mislabelling poses economic, health, legal and environmental implications, says study author Mehrdad Hajibabaei.

"Currently there is no other broadly applicable tool that can identify the species used in both animal and plant natural health products as rapidly and cost-effectively," said Hajibabaei, a U of G integrative biology professor and director of technology development for the Guelph-based Biodiversity Institute of Ontario (BIO).

Up to about 80 per cent of people in developed countries use natural health products, including vitamins, minerals and herbal remedies. In Canada, these products have been regulated since 2004. But regulators face a backlog of licence applications, and thousands of products on the market lack a full product licence. In the U.S. and the U.K., regulatory problems involving natural health products have affected consistency and safety.

Authenticating natural product capsules or tablets -- containing dried fragments rather than whole specimens -- poses challenges.

DNA barcoding allows scientists to use short standardized regions of genetic material to identify species and compare them to reference genetic sequences, said Hajibabaei.

The technique works for all life stages and even for fragments of organisms, allowing scientists to ID even dried contents of a small pill.

"DNA barcoding provides a simple and efficient method for accurate identification and can play a key role in developing a more robust protocol for their regulation," Hajibabaei said.

For the study, researchers tested 95 plant and animal products bought in Toronto and New York City. Samples included capsules, tablets, roots, extracts, teas and shredded products. The researchers also sampled for products containing widely used shark tissue or ginseng.

Fully 81 per cent of natural health products made from animals correctly matched their commercial label. The rest contained everything from cheaper alternatives to fragments of protected species. One product labelled as tiger shark fins actually contained a catfish species.

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DNA barcoding can ID natural health products

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GLOBAL BIOENERGIES Receives the “Most Innovative European Biotech SME” EuropaBio Award

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EVRY, France--(BUSINESS WIRE)--

Global Bioenergies, the industrial biology company developing sustainable routes to light olefins, has been selected by EuropaBio, the organization representing more than 1800 European companies, to receive the most innovative European biotech SME award.

As announced previously, Global Bioenergies had been selected as one of the five nominees contending for the most innovative European biotech SME award bestowed by EuropaBio, the principal organization which represents more than 1800 European biotechnology companies. On September 19th 2012, the final awardees chosen by an expert panel were revealed at the award ceremony held in the European Parliament by Commission Vice President Antonio Tajani, Commissioner for Industry & Entrepreneurship.

Global Bioenergies is proud to announce that it has received this prestigious award which was initially opened to all European biotechnology companies active in fields as diverse as pharmaceuticals, diagnostics, plant science, environment and industrial biology. According to Nathalie Moll, EuropaBio General Secretary, this choice was motivated by the innovations developed by Global Bioenergies, but also by their economic potential and their ability to answer some of our societys most pressing needs. The corresponding EuropaBio announcement can be found under: http://www.EuropaBio.org

About GLOBAL BIOENERGIES

Global Bioenergies is one of the few companies worldwide, and the only one in Europe, that is developing a process to convert renewable resources into hydrocarbons through fermentation. The Company initially focused its efforts on the production of isobutene, one of the most important petrochemical building blocks that can be converted into fuels, plastics, organic glass and elastomers. Global Bioenergies continues to improve the yield of its process and prepares the phase dedicated to pilot testing. The company is also looking to replicate this success with other members of the gaseous olefins family (propylene, ethylene, linear butylenes, butadiene), key molecules at the heart of petrochemical industry. Global Bioenergies is listed on NYSE Alternext Paris (FR0011052257 ALGBE).

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GLOBAL BIOENERGIES Receives the “Most Innovative European Biotech SME” EuropaBio Award

American Physiological Society's latest conference focuses on integrative biology of exercise

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Public release date: 20-Sep-2012 [ | E-mail | Share ]

Contact: Donna Krupa dkrupa@the-aps.org American Physiological Society

BETHESDA, Md. (Sept. 20, 2012) The latest conference to be sponsored by the American Physiological Society (APS) focuses on the molecular mechanisms involved in exercise-mediated physiological changes in the body, including metabolic, cardiovascular, neurological, and dynamic molecular and cellular pathways. Entitled Integrative Biology of Exercise VI, the meeting will be held October 10-13, 2012 in Westminster, Colorado. The full program is available online at http://bit.ly/OrMFtN. An overview of the program is below.

Thursday, October 11, 2012

Plenary Lecture: Toward Personalized Lifestyle Medicine Geoffrey Ginsburg, M.D., Ph.D., of the Duke Institute for Genome Sciences and Policy will deliver this talk on integrating personalized medicine and healthcare.

Symposia I: Integrating Human "Omics" to the Molecular Physiology of Exercise Speakers will discuss pathways and mechanisms involved in exercise-modulated improvements in health, focusing on small molecule metabolites, skeletal muscle gene expression, the proteome and integrative molecular physiology of exercise.

Symposia II: Personalized Exercise Prescription Based Upon Integrative Biology Experts will explore genetic, transcriptomic, phenotypic and pharmacologic considerations in identifying and predicting individual response to exercise regimens.

Symposia III: Mechanisms Behind Adaptations to Physical Activity/Inactivity The session will focus on signaling pathways, gene expression and posttranslational modifications in skeletal muscle remodeling and adaptation in activity and inactivity.

Symposia IV: Acetylation: Linking changes in NAD to Metabolism and Growth This session will provide insights into the role of NAD+ and its role in mitochondrial protein synthesis, metabolism, and metabolic diseases.

Friday, October 12, 2012

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American Physiological Society's latest conference focuses on integrative biology of exercise

Third Rock Ventures Launches MyoKardia with $38 Million to Address Genetic Heart Disease

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SAN FRANCISCO & BOSTON--(BUSINESS WIRE)--

Third Rock Ventures, LLC today announced the formation of MyoKardia, Inc. with a $38 million Series A financing of the company. MyoKardia is developing a pipeline of novel small molecule therapeutics that address key clinical needs for patients with genetic heart disease. The companys first programs include hypertrophic and dilated cardiomyopathy, which together afflict approximately 1 million people in the United States, and for which no novel therapeutics have been brought to market in over a decade. MyoKardias proprietary drug discovery platform brings together advances from the fields of cardiovascular genomics and heart muscle biology to enable its scientists to target certain heart disease at its source. This genetically targeted approach has the potential to revolutionize the treatment of cardiomyopathies, and ultimately a broader spectrum of cardiovascular disease, including heart failure. The company is founded by world leaders in the fields of muscle biology and cardiovascular genetics: James Spudich, Ph.D., Professor of Biochemistry, Stanford University, Leslie Leinwand, Ph.D., Professor of Molecular, Cellular and Developmental Biology, University of Colorado, Christine Seidman, M.D., Professor of Medicine and Genetics, Harvard Medical School and Director of the Cardiovascular Genetics Center at Brigham and Womens Hospital, and Jonathan Seidman, Ph.D., Professor of Genetics, Harvard Medical School.

The last decade has been challenging for those pursuing novel therapeutics in the cardiovascular space, in part because most treatments target symptoms far downstream of the root cause, said Dr.Leinwand. MyoKardias approach addresses this challenge head on by employing genetics to more precisely define the disease and who we want to treat, and by employing cutting-edge muscle biochemistry and a novel platform to determine how we want to treat. Our initial targets are genetic cardiomyopathies, but this could very well be a novel and tractable therapeutic discovery approach to even larger diseases like heart failure.

Abnormalities in the basic unit of heart muscle, called the sarcomere, have been identified as the driving cause for a variety of heart disease, and the most common cause of hypertrophic and dilated cardiomyopathy. Mutations in the proteins of the sarcomere cause disease by rendering the muscle either hyper or hypo contractile. MyoKardias platform brings together recent assay and protein expression advances pioneered by its founders with genetic insights to enable a personalized medicine approach. This allows for the rapid development of mutation-specific sarcomeric allosteric modulators that rebalance contractility, therefore stopping and potentially reversing the course of disease. MyoKardias approach will leverage resident expertise in sarcomere genetics, in-vivo and in-vitro disease models, next-generation biochemical and biophysical assay development, and medicinal chemistry. Together, these capabilities will provide for the efficient progression of multiple programs in DCM, HCM, and other genetic cardiomyopathies and heart disease related to sarcomere dysfunction.

With MyoKardias platform, we have the ability to exquisitely characterize the biochemistry and biophysics of the human mutated sarcomere, said Dr. Spudich. This not only allows us to better understand what drives pathophysiology, it also points us toward potential mutant specific solutions.

Our goal is to provide treatments for patients with genetic diseases for whom the options to date have been profoundly limited, said Charles Homcy, M.D., interim chief executive officer of MyoKardia and venture partner at Third Rock Ventures. With this Series A financing, we can meet our goals. We now have the resources and capabilities to effectively translate the insights of our founders and employees into multiple clinical products that positively impact patient lives.

Hypertrophic and dilated cardiomyopathies, MyoKardias first two focus disease areas, are the most common forms of heart muscle disease and the most common diagnosis leading to cardiac transplantation. More than 60 million people worldwide have cardiomyopathy or carry a cardiomyopathy gene mutation, including approximately 1 million patients in the United States. Despite this large patient population and the persisting unmet clinical need, there is a lack of novel therapeutics being developed that directly target these diseases.

About Genetic Cardiomyopathy

Genetic cardiomyopathies are conditions that arise from mutation in a critical heart muscle protein. Hypertrophic cardiomyopathy (HCM) produces thickening of the heart walls and is best known as a leading cause of sudden cardiac death in young athletes. Dilated cardiomyopathy (DCM) produces weakening of the heart walls and enlargement of the heart chambers. Cardiomyopathy can occur at any age, and more than 30,000 children, from newborns to 18-year-olds, suffer from some form of cardiomyopathy in the United States a patient population comparable to the number of people living with cystic fibrosis.

About MyoKardia, Inc.

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Third Rock Ventures Launches MyoKardia with $38 Million to Address Genetic Heart Disease

Pure Saffron Benefits Produce Glowing, Radiant Skin

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LOS ANGELES, Sept. 20, 2012 /PRNewswire-iReach/ -- Saffron, the most expensive herb in the world and a staple in ancient Indian cuisine and medicine is now being used in skin care. Saffron as an herb is a well-kept secret that not only produces glowing radiant skin but also helps the body fight against cancer.

(Photo: http://photos.prnewswire.com/prnh/20120920/CG77944)

Vedanic's 24KT Pure Gold Parabens-Free Anti-Aging Moisturizer has for the very first time made saffron available as a skin treatment and anti-aging salve. Crafted from hand-picked saffron, almond oil, shea butter, 24KT pure gold, and other premium organic and natural herbs, Vedanic's ayurvedic moisturizer keeps the skin thoroughly nourished and helps heal the skin naturally, without relying on any cancer-causing ingredients. The 24 KT pure gold allows the skin to breathe, providing a rush of oxygen to the epidermis. The saffron herbal formulation is then delivered fast and effectively to the inner skin layers. Results are almost instant.

Vedanic's saffron-infused skincare products, like the 24KT Pure Gold Parabens-Free Anti-Aging Moisturizer, are fast becoming a popular choice at salon and day spas, spa resorts, stores and evn dermatologists because they are not only instantly effective but pure and natural, made in Ecocert approved labs and packaged in US FDA approved facilities.

The traditional ayurvedic benefits of saffron for organic skincare are many. Saffron is also known to make dull skin bright, rough skin smooth, and dark skin light. Because its properties fight bacteria, saffron is also used in acne treatment. Being an anti-aging agent, pure saffron almost immediately tightens the skin and helps close skin pores.

In addition to skin rejuvenation, saffron has a number of other medicinal benefits that herb specialists have called upon for centuries throughout the world. One of the most stunning of these benefits is saffron's anticarcinogenic properties. Saffron has not only been known to prevent cancer, it has actually been known to delay to growth of tumors and slow the spread of cancer.

Vedanic's 24KT Pure Gold Parabens Free Anti Aging Moisturizeris blended with other organic, natural ingredients to create a safe, effective skincare product. While parabens (a known carcinogen and ingredient in most skincare products) is found in 99% of breast cancer tissue, Vedanic's premiere products not only do not have any known carcinogenic chemicals but instead include cancer-fighting saffron and other holistic, beneficial ingredients. Vedanic's products are made from some certified organic and natural herbs. They are not animal tested, have no added artificial colors or perfumes and are only manufactured using fair trade practices and no child labor.

Vedanic believes that clear, radiant skin should be the outgrowth of overall good health. This is why Vedanic is committed to producing skincare that include only the best organic, natural ingredients available. 24KT Pure Gold Parabens-Free Anti-Aging Moisturizer uses the natural healing and medicinal properties of saffron, almond oil, shea butter, and wheatgerm oil, as well as the oxidizing properties of gold, to beautify as well as strengthen and tighten skin. Individuals can use Vedanic's saffron-infused moisturizer throughout the year to protect skin from rough weather and harsh conditions.

Varun Khanna, Vedanic Organic Skincare, 310-925-7957, vedanic.marketing@vedanic.com

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Purple corn extracts show benefits for diabetic’s kidney health

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Compounds in purple corn may protect against the development of the kidney condition diabetic nephropathy, one of the most serious complications related to diabetes, suggests new research.

Scientists from Hallym University in Korea report in the American Journal of Physiology Renal Physiology that anthocyanin-rich purple corn may inhibit multiple pathways involved in the development of diabetic nephropathy.

The research also suggests that supplementation with purple corn anthocyanins may be an important strategy in preventing renal vascular disease in type-2 diabetes, they added.

The researchers cultured cells in the lab in solutions of varying concentrations of anthocyanins, and then assessed for level of monocyte-endothelial cell adhesion, a major factor in the hardening of the glomerulus in the kidney of diabetics (diabetic glomerulosclerosis). This was corroborated with data from experiments with lab mice fed a diet supplemented with the purple corn extracts for eight weeks.

Results showed that the anthocyanins inhibited pathways that led to diabetic glomerulosclerosis, as well as the induction of some inflammatory processes in the mice.

Source: American Journal of Physiology Renal Physiology Published online ahead of print, doi: 10.1152/ajprenal.00106.2012 Purple corn anthocyanins inhibit diabetes-associated glomerular monocyte activation and macrophage infiltration Authors: M-K. Kang, J. Li, J-L. Kim, J-H. Gong, et al.

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Purple corn extracts show benefits for diabetic’s kidney health

Hospitals, Healthcare Providers to Benefit from New Premier Agreements for Digital Pathology Systems, Accessories and …

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CHARLOTTE, N.C.--(BUSINESS WIRE)--

The Premier healthcare alliance today announced a new agreement for digital pathology systems, accessories and service has been awarded to DigiPath Inc. a small business enterprise, of Henderson, Nev.

Effective August 1, 2012, the agreement is available to acute care and continuum of care members of Premier.

About the Premier healthcare alliance, Malcolm Baldrige National Quality Award recipient

Premier is a performance improvement alliance of more than 2,600 U.S. hospitals and 88,000-plus other sites using the power of collaboration and technology to lead the transformation to coordinated, high-quality, cost-effective care. Owned by hospitals, health systems and other providers, Premier operates a leading healthcare purchasing network with more than $4 billion in annual savings. Premier also maintains the nation's largest clinical, financial and outcomes database with information on 1 in 4 patient discharges. A world leader in delivering measurable improvements in care, Premier works with the Centers for Medicare & Medicaid Services. Headquartered in Charlotte, N.C., Premier also has an office in Washington. https://www.premierinc.com. Stay connected on Facebook, Twitter and YouTube.

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Chris Powell Endorsed Product Line Named Favorite New Product

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SCOTTSDALE, AZ--(Marketwire - Sep 18, 2012) - Last night, Vemma Nutrition Company won two prestigious awards at the 2012 American Business Awards at a gala event held in San Francisco. Endorsed by TV Celebrity Transformation Specialist, Chris Powell, the Vemma Bod- healthy weight management product line won the People's Choice Stevie Award for Favorite Consumer Product or Service. In addition, the Vemma Bod- App received a Gold Stevie Award in the Lifestyle App category.

The award trophies were presented to Vemma at a gala ceremony on September 17th at the Julia Morgan Ballroom in downtown San Francisco, CA. They were presented as part of the second (and final) phase of judging for the 2012 American Business Awards.

To receive a coveted crystal People's Choice Award, Vemma Bod- received the highest number of votes in the consumer products and services category. A total of 98,000 consumer votes were cast in 30 categories.

"These are awesome products that are helping people see real results, so it's great that they're getting these accolades," says Chris Powell. "People really love the taste and what these products do for their body."

Other notable People's Choice winners included Apple (for the iPad 2 and iPhone 4S), Humana health insurance, and Appsbar, a free online apps building service.

The Vemma Bod- App -- which features daily tips, support and inspiration from Heidi Powell, Vemma Bod- Spokesperson, Personal Trainer and Life Coach -- was judged by executives from a 270-person panel and ultimately selected as the Gold winner (the competition's highest honor) in the lifestyle app category.

More than 3,000 entries were submitted in this year's competition. Other Gold Stevie award winners included favorite American brands such as NASCAR, Verizon Wireless, Ford Motor Company and Hilton Hotels and Resorts.

The Vemma Bod- product line launched in January 2012, sparking the company's first million dollar sales day. Vemma Founder and CEO BK Boreyko commented, "It's been an exciting year with the Vemma Bod- launch and we are honored with these wins at the Stevies. These awards are a reflection of the hard work of our stellar staff and the talented Brand Partners who represent our company with such integrity. I sincerely thank the Vemma Brand Partners and Vemma Bod- consumers for choosing us as their favorite consumer product."

The American Business Awards are the nation's premier business awards for companies of all sizes and industries. For more information about The American Business Awards and a complete list of winners, go to: http://www.stevieawards.com/aba.

About Vemma Founded in 2004 by BK Boreyko, Vemma Nutrition Company is rapidly growing as one of the premier industry leaders specializing in premium liquid nutrition. Every day, thousands of people join the company's mission to make a positive difference in the lives of others through the sharing of the clinically studied Vemma formula. The Vemma brands, including Verve, a healthy energy drink, coupled with the company's rewarding business opportunity help people to live a better quality of life, both physically and financially. Vemma is headquartered in Scottsdale, Arizona and distributes its products through a global network of independent Brand Partners operating in approximately 50 countries. For more information about Vemma visit the company's social media newsroom.

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Longevity Revolution Means Broader Role for Chiropractice

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Media Release

Date: 20th September 2012

Longevity Revolution Means Broader Role for Chiropractice Australasian Meeting Told

The longevity revolution epitomised by ageing baby boomers means a broader role for chiropractors in helping people with decreased muscle or bone density and balance issues which add to the risk of falling, a conference of New Zealand, Australian and International chiropractors in Auckland was told this week.

The conference during the weekend (14th-16th September) organised by the New Zealand College of Chiropractic heard that the implications of the baby boomer generation reaching retirement age meant healthcare providers needed a better understanding of the unique role chiropractic can play. Delegates learned about the various chiropractic techniques best suited to the elderly, how to effectively manage any rare associated risks and also a better idea of the expectations that seniors have of their care.

Dr Graham Dobson, chiropractor, Director of the Technique Department at the New Zealand College of Chiropractic told the meeting that chiropractic had: `a vital part to play in reducing pain and the need for pharmaceuticals, increasing joint mobility and improved overall quality of life by helping to maintain function and a positive attitude.

He noted that chiropractic care has often been associated only with the management of limited musculoskeletal disorders by the application of spinal manipulative therapy but that increasingly chiropractors were using multiple techniques to assist the patient as a whole by addressing the nervous system, not only his or her musculoskeletal symptoms. Research is beginning to point at chiropractic as having a role to play in the multi disciplinary management of people with conditions such as sarcopenia (muscle loss) and osteoporosis.

However, Dr Dobson warned that it is important for chiropractors to evaluate older patients carefully to take account of factors such as osteoporosis, multiple interactions of prescription medications as well as the risk of falls.

Research into how chiropractic care for older people may reduce injuries and even deaths from falls is being conducted by Auckland University and the Centre for Chiropractic Research (CCR) at the New Zealand College of Chiropractic.

According to Chiropractor, PhD candidate and principal investigator of the study Dr Kelly Holt, falls often occur due to a decline in nervous system function with advancing age. This can lead to a loss of balance, or poor control of the limbs, which dramatically increases the risk of falling.

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Longevity Revolution Means Broader Role for Chiropractice