Charged graphene gives DNA a stage to perform molecular gymnastics

DNA interacts with charged graphene and contorts into sequence-specific shapes when the charge is changed. Credit: Photo courtesy Alek Aksimentiev

When Illinois researchers set out to investigate a method to control how DNA moves through a tiny sequencing device, they did not know they were about to witness a display of molecular gymnastics.

Fast, accurate and affordable DNA sequencing is the first step toward personalized medicine. Threading a DNA molecule through a tiny hole, called a nanopore, in a sheet of graphene allows researchers to read the DNA sequence; however, they have limited control over how fast the DNA moves through the pore. In a new study published in the journal Nature Communications, University of Illinois physics professor Aleksei Aksimentiev and graduate student Manish Shankla applied an electric charge to the graphene sheet, hoping that the DNA would react to the charge in a way that would let them control its movement down to each individual link, or nucleotide, in the DNA chain.

"Ideally, you would want to step the DNA through the nanopore one nucleotide at a time," said Aksimentiev. "Take a measurement and then have another nucleotide in the sensing hole. That's the goal, and it hasn't been realized yet. We show that, to some degree, we can control the process by charging the graphene."

The researchers found that a positive charge in the graphene speeds up DNA movement through the nanopore, while a negative charge stops the DNA in its tracks. However, as they watched, the DNA seemed to dance across the graphene surface, pirouetting into shapes they had never seen, specific to the sequence of the DNA nucleotides.

"It reminds me of Swan Lake," Aksimentiev said. "It's very acrobatic. We were very surprised by the variety of DNA conformations that we can observe at the surface of graphene when we charge it. There is one sequence that starts out laying down on the surface, and when we change the charge, they all tilt on the side like they are doing a one-armed push-up. Then we also have nucleotides that would lay back, or go up like a ballerina en pointe."

Aksimentiev hypothesizes that the conformations are so different and so specific to the sequence because each nucleotide has a slightly different distribution of electrons, the negatively charged parts of the atoms. There is even a visible difference when a nucleotide is methylated, a tiny chemical change that can turn a gene on or off.

By switching the charge in the graphene, the researchers can control not only the DNA's motion through the pore, but also the shape the DNA contorts into.

"Because it's reversible, we can force it to adopt one conformation and then force it to go back. That's why we call it gymnastics," Aksimentiev said.

The researchers extensively used the Blue Waters supercomputer at the National Center for Supercomputing Applications, housed at the University of Illinois. They mapped each individual atom in the complex DNA molecule and ran numerous simulations of many different DNA sequences. Supercomputing power was essential to carrying out the work, Aksimentiev said.

"This is a really computationally intensive project," he said. "Having access to Blue Waters was essential because with the sheer number of simulations, we would not have been able to finish them. It would have taken too long."

The next step is to combine a charged nanopore setup with a sensor to build a DNA sequencing device that would incorporate both motion control and nucleotide recognition. The researchers also hope to explore the unexpected conformational changes for insights into epigenetics, the field that studies how genes are expressed and moderated.

"DNA is much more complicated than just a double helix. It's a complex molecule that has many properties, and we are still uncovering them," Aksimentiev said.

Video animation of DNA dancing as the graphene charge changes:


Source: University of Illinois at Urbana-Champaign

Caught by a hair: Quick, new identification of hair may help crime fighters

Lily Huang crushes up the human hair prior to testing. Credit: Image courtesy of Queen's University

Crime fighters could have a new tool at their disposal following promising research by Queen's professor Diane Beauchemin.

Dr. Beauchemin (Chemistry) and student Lily Huang (MSc'15) have developed a cutting-edge technique to identify human hair. Their test is quicker than DNA analysis techniques currently used by law enforcement. Early sample testing at Queen's produced a 100 per cent success rate.

"My first paper and foray into forensic chemistry was developing a method of identifying paint that could help solve hit and run cases," explains Dr. Beauchemin. "Last year, Lily wanted to research hair analysis, so I started working in that area."

Blood samples are often used to identify gender and ethnicity, but blood can deteriorate quickly and can easily be contaminated. Hair, on the other hand, is very stable. Elements in hair originate from sweat secretions that alter with diet, ethnicity, gender, the environment and working conditions.

Dr. Beauchemin's process takes 85 seconds to complete and involves grinding up the hair, burning it and then analyzing the vapour that is produced.

"Our analysis process is very robust and can be used universally," says Ms. Huang. "One of our samples even included dyed hair and the test was 100 per cent accurate. The test was able to distinguish East Asians, Caucasians and South Asians."

Dr. Beauchemin says she has contacted law enforcement agencies about using the new technology. She is also planning to collect more hair samples and continue her research with a goal of pinpointing where exactly in the world the hair sample is from, to look for more ethnicities and determine specific age.

Source: Queen's University

Blazing car murder of 1930 investigated

Slide with Blazing Car victim's sample on it. Sample taken by Sir Bernard Spilsbury.
Credit: University of Leicester

University of Leicester leads collaboration with Northumbria University, Northamptonshire Police and The Royal London Hospital Museum, in investigation of the Blazing Car Murder of 1930

A forensic team from the University of Leicester and Northumbria University has spearheaded an investigation which has shed new light on a murder case from 1930.

A team from the University of Leicester, led by Dr John Bond OBE from the Department of Chemistry and Dr Lisa Smith from the Department of Criminology worked with colleagues from Northumbria University, Northamptonshire Police and The Royal London Hospital Museum to tackle the riddle of the 'Blazing Car Murder' from over 80 years ago.

The case involved the murder of a male in a car fire in Hardingstone, Northamptonshire, on 6 November 1930. Alfred Rouse was convicted, and later hanged, at Bedford Gaol in March 1931, for murdering his victim who to this day, has not been identified.

At the time, a post mortem examination was carried out in the garage of the local public house by the Home Office-appointed pathologist Sir Bernard Spilsbury, working alongside another local pathologist.

Sir Spilsbury reported that lavender coloured material and light brown hair were found at the scene. It was further documented that the victim's jawbone was removed to assist with possible identification and tissue samples taken for microscopical examination.

Two of these tissue samples are still in existence and archived in The Royal London Hospital Museum: one from the prostate to confirm the sex of the victim, and another from the lung to determine whether or not the victim was already dead before the fire was started.

In recent months, attention has turned to the fact that a man named William Briggs left his family home in London to attend a doctor's appointment at around the same time the crime was committed -- and was never seen or heard of again.

As part of their family ancestry research, the relatives of William Briggs wanted to verify earlier generations' belief that their ancestor may have been Rouse's car murder victim.

Last year, a number of William Briggs's relatives approached Northamptonshire Police in an attempt to put the 83-year-old mystery to rest and finally reveal the identity of the victim.

They met with the Force's curator and archivist Richard Cowley, discussed the story of the murder and were shown artefacts relating to the crime which, at the time received worldwide attention.

With the help of Northamptonshire Police, the family contacted University of Leicester academic Dr John Bond OBE. He and Dr Lisa Smith negotiated with The Royal London Hospital museum to allow one of the remaining tissue samples to be examined.

The slide was released with the approval of Professor Richard Trembath, at Queen Mary College University of London. The slide originates from the old Department of Forensic Medicine which formed part of The London Hospital Medical College. The College was merged with Queen Mary College in 1995.

The University of Leicester team considered whether there might just be enough mitochondrial DNA (mtDNA) left on the slide to get a profile to compare with mtDNA from the family.

Mitochondrial DNA is wholly inherited from the maternal line so it is essential to have an unbroken maternal line of descendants to test.

University of Leicester worked with the Northumbria University Centre for Forensic Science and Dr Eleanor Graham, a former member of staff at the University of Leicester, and Victoria Barlow to carry out DNA analysis on the samples to see if there was a match from the sample and the relatives.

Fortunately, the scientists obtained a full single male mtDNA profile from the slide to compare to the family.

Dr John Bond, from the University of Leicester said: "It's been very interesting and rewarding working on such a famous, local murder case. It was quite a unique investigation to be involved in, as the perpetrator had been identified long ago and brought to justice while the victim's identity remained unknown.

"It was a great example of how the scientific and criminological expertise at the University of Leicester and Northumbria University, working together with the police, could provide answers to this family after 83 years."

Detective Chief Superintendent Paul Phillips from Northamptonshire Police said: "From our perspective this is a closed case, the offender Alfred Rouse was convicted of murder and hanged, but this has been a long-standing mystery in Northamptonshire as the identity of the victim has never been established.

"Our work at Northamptonshire Police is victim focused so I was delighted to learn of new opportunities to establish the identity of the victim through the development of forensic science."

Dr Eleanor Graham from Northumbria University stated: "Projects such as this highlight the fact that forensic DNA analysis is not confined to 'catching criminals'. DNA analysis also has a critical role to play in the identification of those who have been killed during criminal acts, accidents or natural disasters, which have occurred recently, or many years ago."

The result is due to be revealed to the family on the BBC's The One Show on a date to be fixed.

Blazing Car Murder background:

Alfred Rouse sustained a head wound in the First World War, which left him with a personality disorder, to the point that he was described as 'a promiscuous rake with an enormous sexual appetite'.

Rouse was a commercial traveller who went all around the country and his promiscuous lifestyle resulted in him facing severe financial problems.

As a consequence, Rouse devised a plan to murder a homeless tramp who would not be missed by anyone which would enable him to stage his own death in a car accident and then disappear to start a new life free from financial restriction.

To that end, Rouse rendered his victim unconscious, placed him in the driver's seat of his car and set the car alight.

Rouse was making his way from the scene but bumped into two local youths keen to see what was going on and take part in some late Bonfire Night celebrations.

This initial contact eventually led to Rouse's arrest. He was convicted at Northampton Assizes and hanged in Bedford on 10 March 1931.

The local Herald newspaper suggested that the identity of Rouse's victim 'would likely remain a mystery forever.' But will it………..?

Source: University of Leicester

Sniffing-out smell of disease in feces: 'Electronic nose' for rapid detection of Clostridum difficile infection

This image depicts from lef to right Dr Martha Clokie, Professor Andy Ellis and Professor Paul Monks from the University of Leicester with the mass spectrometer. Credit: University of Leicester

A fast-sensitive "electronic-nose" for sniffing the highly infectious bacteria C-diff, that causes diarrhea, temperature and stomach cramps, has been developed by a team at the University of Leicester.

Using a mass spectrometer, the research team has demonstrated that it is possible to identify the unique 'smell' of C-diff which would lead to rapid diagnosis of the condition.

What is more, the Leicester team say it could be possible to identify different strains of the disease simply from their smell -- a chemical fingerprint -- helping medics to target the particular condition.

The research is published on-line in the journal Metabolomics.

Professor Paul Monks, from the Department of Chemistry, said: "The rapid detection and identification of the bug Clostridium difficile (often known as C-diff) is a primary concern in healthcare facilities. Rapid and accurate diagnoses are important to reduce Clostridum difficile infections, as well as to provide the right treatment to infected patients.

"Delayed treatment and inappropriate antibiotics not only cause high morbidity and mortality, but also add costs to the healthcare system through lost bed days. Different strains of C. difficile can cause different symptoms and may need to be treated differently so a test that could determine not only an infection, but what type of infection could lead to new treatment options."

The new published research from the University of Leicester has shown that is possible to 'sniff' the infection for rapid detection of Clostridium difficile. The team have measured the Volatile Organic Compounds (VOCs) given out by different of strains of Clostridium difficile and have shown that many of them have a unique "smell." In particular, different strains show different chemical fingerprints which are detected by a mass spectrometer.

The work was a collaboration between University chemists who developed the "electronic-nose" for sniffing volatiles and a colleague in microbiology who has a large collection of well characterised strains of Clostridium difficile.

The work suggests that the detection of the chemical fingerprint may allow for a rapid means of identifying C. difficile infection, as well as providing markers for the way the different strains grow.

Professor Monks added: "Our approach may lead to a rapid clinical diagnostic test based on the VOCs released from faecal samples of patients infected with C. difficile. We do not underestimate the challenges in sampling and attributing C. difficile VOCs from fecal samples."

Dr Martha Clokie, from the Department of Microbiology and Immunology, added: "Current tests for C. difficile don't generally give strain information -- this test could allow doctors to see what strain was causing the illness and allow doctors to tailor their treatment."

Professor Andy Ellis, from the Department of Chemistry, said: "This work shows great promise. The different strains of C-diff have significantly different chemical fingerprints and with further research we would hope to be able to develop a reliable and almost instantaneous tool for detecting a specific strain, even if present in very small quantities."

Source: University of Leicester

New biometric watches use light to non-invasively monitor glucose, dehydration, pulse

This schematic diagram shows how the new system can be used to measure a person's glucose levels noninvasively. Credit: Biomedical Optics Express

Monitoring a patient's vital signs and other physiological parameters is a standard part of medical care, but, increasingly, health and fitness-minded individuals are looking for ways to easily keep their own tabs on these measurements. Enter the biometric watch.

In a pair of papers published in The Optical Society's (OSA) open-access journal Biomedical Optics Express, groups of researchers from the Netherlands and Israel describe two new wearable devices that use changing patterns of scattered light to monitor biometrics: one tracks glucose concentration and dehydration levels, and the other monitors pulse.

The glucose sensor is the first wearable device that can measure glucose concentration directly but noninvasively, the authors say.
And while other wearable devices have been made to monitor pulse, the authors claim their new design would be less sensitive to errors when the wearer is in motion, for example while walking or playing sports

Both of the watches described in the two papers make use of the so-called "speckle" effect, the grainy interference patterns that are produced on images when laser light reflects from an uneven surface or scatters from an opaque material. When the material that is scattering the light is moving -- say, in the case of blood flowing through the circulatory system -- "the speckle pattern changes with changes in the flow," explained biomedical engineer Mahsa Nemati, a graduate student in the Optics Research Group at the Delft University of Technology in the Netherlands and the lead author of the Biomedical Optics Express paper on monitoring pulse. Those light variations are a valuable source of information, she says.

The 'Holy Grail' of Diagnostics

In the first paper, bioengineer Zeev Zalevsky of Israel's Bar-Ilan University and his colleagues describe a new wearable biometric system that uses the speckle effect to directly monitor the glucose concentration in the bloodstream, as well as the wearer's relative hydration level.

"Glucose is the holy grail of the world of biomedical diagnostics, and dehydration is a very useful parameter in the field of wellness, which is one of our main commercial aims," Zalevsky said.

The watch-like device consists of a laser to generate a wavefront of light that illuminates a patch of skin on the wrist near an artery, and a camera that measures changes over time in the light that is backscattered off the skin. Unlike other chemicals present in the blood, glucose exhibits a so-called Faraday effect. This means that in the presence of an external magnetic field (generated by a magnet attached to the device) the glucose molecule alters the polarization of the wavefront and thus influences the resulting speckle patterns. 
Analyzing these changing patterns provides a direct measurement of the glucose concentration. Because one of the main signs of mild to moderate dehydration is muscle weakness, which will alter the strength of the signals, the same device can also be used to indicate the relative dehydration level of the user as it changes over time.

Zalevsky and his colleagues are now working to reduce the margin of error in the device's readings. "Around 96 percent of our in vivo measurements were within a range of 15 percent deviation from the readout of a medical reference glucometer device," Zalevsky noted. "The main factor for errors now is the stability of our device on the wrist of the user. We are currently investing efforts in deriving proper calibration and motion cancellation procedures that will allow us to reduce this sensitivity."

Zalevsky says this is the first step toward non-invasive, continuous in vivo measurement of glucose that is based on sensing an effect that is directly related to glucose concentration. The team expects a commercial version of the device to reach the market within two to three years.

Pulse Tracker

In the second Biomedical Optics Express paper, Nemati and her colleagues at Delft and at Phillips Research developed a method that could be used to monitor pulse non-invasively with a sensor that isn't thrown off by the wearer's movement.

Using simulated heart beats generated in milk and measurements performed on the finger of a volunteer, they found that speckle changes can be used to accurately measure flow pulsations -- that is, the heart rate -- even when the light source used to create the speckle pattern is also moving, as would be the case with a wearable biometric sensor. The researchers found that just a couple of pixels from the image were sufficient to extract the pulse rate.

"This paper shows for the first time that a speckle pattern generated from a flowing liquid can give us the pulsation properties of the flow in spite of motion-induced artifacts," Nemati said. "Sophisticated optics is not necessary to implement this, so the costs for devices can be kept low. Another advantage is that the devices can be non-contact or far from the sample," she added.

The team is currently working with companies to integrate their motion-friendly pulse-monitoring technique into existing sensors, for potential use clinically as well as in sports, Nemati said.

Source: The Optical Society

A lab in your pocket: Using CAD to load dozens of tests on a lab-on-a-chip

Two computer-generated configurations for routing a droplet through multiple lab-on-a-chip diagnostic tests, many more than are currently possible using manual methods. The software was developed by Michigan Tech's Shiyan Hu and Chen Liao. The figure is reproduced with permission of IEEE Transactions on NanoBioscience. Credit: Chen Liao and Shiyan Hu

When you get sick, your physician may take a sample of your blood, send it to the lab and wait for results. In the near future, however, doctors may be able to run those tests almost instantly on a piece of plastic about the size of credit card.

These labs-on-a-chip would not only be quick -- results are available in minutes -- but also inexpensive and portable. They could be used miles from the nearest medical clinic to test for anything from HIV to diabetes. But as powerful as they may be, they could be far better, says Shiyan Hu, an associate professor of electrical and computer engineering at Michigan Technological University.

Generally, a lab-on-a-chip (LOC) can run no more than a test or two. That's because the chips are designed manually, says Hu. If the LOC were made using computer-aided design, you could run dozens of tests with a single drop of blood.

"In a very short time, you could test for many conditions," he said. "This really would be an entire lab on a chip."

With PhD student Chen Liao, Hu has taken the first step. "We have developed software to design the hardware," he said. Their work focuses on routing the droplet of blood or other fluid through each test on the chip efficiently while avoiding any chip contamination.

"It has taken us four years to do the software, but to manufacture the LOC would be inexpensive," Hu said. "The materials are very cheap, and the results are more accurate than a conventional lab's."

Ultimately, Hu aims to fabricate their own biochip using their software.

Their work was featured on the cover of the March edition of IEEE Transactions on Nanobiosciences and described in the article "Physical-Level Synthesis for Digital Lab-On-a-Chip Considering Variation, Contamination, and Defect." Liao was partially supported by an A. Richard Newton Graduate Scholarship, awarded by the Design Automation Conference.

Source: Michigan Technological University

Smartphone sensors leave trackable fingerprints

Example demonstrating how accelerometer data shared with separate traffic and health applications could indicate Bob's location. Credit: Image courtesy of University of Illinois College of Engineering

Fingerprints -- those swirling residues left on keyboards and doorknobs -- are mostly invisible. They can affirm your onetime presence, but they cannot be used to track your day-to-day activities.

They cannot tell someone in real time that after exercising at the gym, you went to office in a bus and played video games during lunch. But what if our hand-held electronics are leaving real-time fingerprints instead? Fingerprints that are so intrinsic to the device that, like our own, they cannot be removed?

Research by Associate Professor Romit Roy Choudhury and graduate students Sanorita Dey and Nirupam Roy has demonstrated that these fingerprints exist within smartphone sensors, mainly because of imperfections during the hardware manufacturing process.

In some ways, it's like cutting out sugar cookies. Even using the same dinosaur-shaped cutter, each cookie will come out slightly different: a blemish here, a pock there. For smartphone sensors, these imperfections simply occur at the micro- or nanoscale.

Their findings were published at the Network and Distributed System Security Symposium (NDSS), a major conference on wireless and web security, held last February in San Diego. 

The research also won the best poster award at the HotMobile international workshop in 

2013.

The researchers focused specifically on the accelerometer, a sensor that tracks three-dimensional movements of the phone -- essential for countless applications, including pedometers, sleep monitoring, mobile gaming -- but their findings suggest that other sensors could leave equally unique fingerprints.

"When you manufacture the hardware, the factory cannot produce the identical thing in millions," Roy said. "So these imperfections create fingerprints."

Of course, these fingerprints are only visible when accelerometer data signals are analyzed in detail. Most applications do not require this level of analysis, yet the data shared with all applications -- your favorite game, your pedometer -- bear the mark. Should someone want to perform this analysis, they could do so.

The researchers tested more than 100 devices over the course of nine months: 80 standalone accelerometer chips used in popular smartphones, 25 Android phones, and 2 tablets.

The accelerometers in all permutations were selected from different manufacturers, to ensure that the fingerprints weren't simply defects resulting from a particular production line.

With 96 percent accuracy, the researchers could discriminate one sensor from another.

"We do not need to know any other information about the phone -- no phone number or SIM card number," Dey said. "Just by looking at the data, we can tell you which device it's coming from. It's almost like another identifier."

In the real world, this suggests that even when a smartphone application doesn't have access to location information (by asking "this application would like to use your current location"), there are other means of identifying the user's activities. It could be obtained with an innocuous-seeming game or chatting service, simply by recording and sending accelerometer data. There are no regulations mandating consent.

To collect the data, the researchers -- as with any would-be attacker -- needed to sample the accelerometer data. Each accelerometer was vibrated using a single vibrator motor -- like those that buzz when a text message is received -- for two-second intervals. During those periods, the accelerometer detected the movement and the readings were transmitted to a supervised-learning tool, which decoded the fingerprint.

"Even if you erase the app in the phone, or even erase and reinstall all software," Roy said, "the fingerprint still stays inherent. That's a serious threat."

At this point, however, there is no absolute solution. Smartphone cases made of rubber or plastic do little to mask the signal. Deliberately injecting white noise in the sensor data can smudge the fingerprint, but such noise can also affect the operation of the application, making your pedometer inaccurate and functionally useless.

If accelerometer data were processed directly on the phone or tablet, rather than on the cloud, the fingerprint could be scrubbed before sending information to the application.

That is, the pedometer application might only receive basic information like "300 steps taken," rather than receiving the raw accelerometer data. This, however, imposes a load on the phone's processor and, more importantly, reduces the phone's battery life.

The research also suggests that other sensors in the phone -- gyroscopes, magnetometers, microphones, cameras, and so forth -- could possess the same types of idiosyncratic differences. So even if, at a large scale, the accuracy of accelerometer fingerprints diminishes, when combined with prints from other sensors, an attack could be even more precise.

"Imagine that your right hand fingerprint, by some chance, matches with mine," Roy Choudhury said. "But your left-hand fingerprint also matching with mine is extremely unlikely. So even if accelerometers don't have unique fingerprints across millions of devices, we believe that by combining with other sensors such as the gyroscope, it might still be possible to track a particular device over time and space."

For smartphone users and e-book readers, smartwatch wearers and tablet devotees, perhaps the most critical take-home message, in the short run anyway, is the importance of vigilance.

"Don't share your accelerometer data without thinking about how legitimate or how secure that application is," Dey said. "Even if it's using only the sensor data, still it can attack you in some way. The consumer should be aware."

Source: University of Illinois College of Engineering