A handheld diagnostic device that Massachusetts General Hospital (MGH) investigators first developed to diagnose cancer has been adapted to rapidly diagnose tuberculosis (TB) and other important infectious bacteria. Two papers describe portable devices that combine microfluidic technology with nuclear magnetic resonance (NMR) to not only diagnose these important infections but also determine the presence of antibiotic-resistant bacterial strains.
‘Rapidly identifying the pathogen responsible for an infection and testing for the presence of resistance are critical not only for diagnosis but also for deciding which antibiotics to give a patient,’ says Ralph Weissleder, MD, PhD, director of the MGH Center for Systems Biology (CSB) and co-senior author of both papers. ‘These described methods allow us to do this in two to three hours, a vast improvement over standard culturing practice, which can take as much as two weeks to provide a diagnosis.’
Investigators at the MGH CSB previously developed portable devices capable of detecting cancer biomarkers in the blood or in very small tissue samples. Target cells or molecules are first labelled with magnetic nanoparticles, and the sample is then passed through a micro NMR system capable of detecting and quantifying levels of the target. But initial efforts to adapt the system to bacterial diagnosis had trouble finding antibodies – the detection method used in the earlier studies – that would accurately detect the specific bacteria. Instead the team switched to targeting specific nucleic acid sequences.
The system detects DNA from the tuberculosis bacteria in small sputum samples. After DNA is extracted from the sample, any of the target sequence that is present is amplified using a standard procedure, then captured by polymer beads containing complementary nucleic acid sequences and labelled with magnetic nanoparticles with sequences that bind to other portions of the target DNA. The miniature NMR coil incorporated into the device – which is about the size of a standard laboratory slide – detects any TB bacterial DNA present in the sample.
Tests of the device on samples from patients known to have TB and from healthy controls identified all positive samples with no false positives in less than three hours. Existing diagnostic procedures can take weeks to provide results and can miss up to 40 percent of infected patients. Results were even stronger for patients infected with both TB and HIV – probably because infection with both pathogens leads to high levels of the TB bacteria – and specialized nucleic acid probes developed by the research team were able to distinguish treatment-resistant bacterial strains.
Another paper describes a similar system using ribosomal RNA (rRNA) – already in use as a bacterial biomarker – as a target for nanoparticle labelling. The investigators developed both a universal nucleic acid probe that detects an rRNA region common to many bacterial species and a set of probes that target sequences specific to 13 clinically important pathogens, including Streptococcus pneumoniae, Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA).
The device was sensitive enough to detect as few as one or two bacteria in a 10 ml blood sample and to accurately estimate bacterial load. Testing the system on blood samples from patients with known infections accurately identified the particular bacterial species in less than two hours and also detected two species that had not been identified with standard culture techniques.
While both systems require further development to incorporate all steps into sealed, stand-alone devices, reducing the risk of contamination, Weissleder notes that the small size and ease of use of these devices make them ideal for use in developing countries. ‘The magnetic interactions that pathogen detection is based on are very reliable, regardless of the quality of the sample, meaning that extensive purification – which would be difficult in resource-limited setting – is not necessary. The ability to diagnose TB in a matter of hours could allow testing and treatment decisions within the same clinic visit, which can be crucial to controlling the spread of TB in developing countries.’ Massachusetts General Hospital

In the summer of 1968, a new strain of influenza appeared in Hong Kong. This strain, known as H3N2, spread around the globe and eventually killed an estimated 1 million people.
A new study from MIT reveals that there are many strains of H3N2 circulating in birds and pigs that are genetically similar to the 1968 strain and have the potential to generate a pandemic if they leap to humans. The researchers, led by Ram Sasisekharan, the Alfred H. Caspary Professor of Biological Engineering at MIT, also found that current flu vaccines might not offer protection against these strains.
‘There are indeed examples of H3N2 that we need to be concerned about,’ says Sasisekharan, who is also a member of MIT’s Koch Institute for Integrative Cancer Research. ‘From a pandemic-preparedness point of view, we should potentially start including some of these H3 strains as part of influenza vaccines.’
The study also offers the World Health Organization and public-health agencies’ insight into viral strains that should raise red flags if detected.
In the past 100 years, influenza viruses that emerged from pigs or birds have caused several notable flu pandemics. When one of these avian or swine viruses gains the ability to infect humans, it can often evade the immune system, which is primed to recognise only strains that commonly infect humans.
Strains of H3N2 have been circulating in humans since the 1968 pandemic, but they have evolved to a less dangerous form that produces a nasty seasonal flu. However, H3N2 strains are also circulating in pigs and birds.
Sasisekharan and his colleagues wanted to determine the risk of H3N2 strains re-emerging in humans, whose immune systems would no longer recognise the more dangerous forms of H3N2. This type of event has a recent precedent: In 2009, a strain of H1N1 emerged that was very similar to the virus that caused a 1918 pandemic that killed 50 million to 100 million people.
‘We asked if that could happen with H3,’ Sasisekharan says. ‘You would think it’s more readily possible with H3 because we observe that there seems to be a lot more mixing of H3 between humans and swine.’
In the new study, the researchers compared the 1968 H3N2 strain and about 1,100 H3 strains now circulating in pigs and birds, focusing on the gene that codes for the viral haemagglutinin (HA) protein.
After comparing HA genetic sequences in five key locations that control the viruses’ interactions with infected hosts, the researchers calculated an ‘antigenic index’ for each strain. This value indicates the percentage of these genetic regions identical to those of the 1968 pandemic strain and helps determine how well an influenza virus can evade a host’s immune response.
The researchers also took into account the patterns of attachment of the HA protein to sugar molecules called glycans. The virus’ ability to attach to glycan receptors found on human respiratory-tract cells is key to infecting humans.
Seeking viruses with an antigenic index of at least 49 percent and glycan-attachment patterns identical to those of the 1968 virus, the research team identified 581 H3 viruses isolated since 2000 that could potentially cause a pandemic. Of these, 549 came from birds and 32 from pigs.
The researchers then exposed some of these strains to antibodies provoked by the current H3 seasonal-flu vaccines. As they predicted, these antibodies were unable to recognise or attack these H3 strains. Of the 581 HA sequences, six swine strains already contain the standard HA mutations necessary for human adaptation, and are thus capable of entering the human population either directly or via genetic reassortment, Sasisekharan says.
‘One of the amazing things about the influenza virus is its ability to grab genes from different pools,’ he says. ‘There could be viral genes that mix among pigs, or between birds and pigs.’
Sasisekharan and colleagues are now doing a similar genetic study of H5 influenza strains. The H3 study was funded by the National Institutes of Health and the National Science Foundation. MIT

Scientists at Washington University School of Medicine in St. Louis have helped identify many of the biomarkers for Alzheimer’s disease that could potentially predict which patients will develop the disorder later in life. Now, studying spinal fluid samples and health data from 201 research participants at the Charles F. and Joanne Knight Alzheimer’s Disease Research Center, the researchers have shown the markers are accurate predictors of Alzheimer’s years before symptoms develop.
‘We wanted to see if one marker was better than the other in predicting which of our participants would get cognitive impairment and when they would get it,’ said Catherine Roe, PhD, research assistant professor of neurology. ‘We found no differences in the accuracy of the biomarkers.’
The researchers evaluated markers such as the buildup of amyloid plaques in the brain, newly visible thanks to an imaging agent developed in the last decade; levels of various proteins in the cerebrospinal fluid, such as the amyloid fragments that are the principal ingredient of brain plaques; and the ratios of one protein to another in the cerebrospinal fluid, such as different forms of the brain cell structural protein tau.
The markers were studied in volunteers whose ages ranged from 45 to 88. On average, the data available on study participants spanned four years, with the longest recorded over 7.5 years.
The researchers found that all of the markers were equally good at identifying subjects who were likely to develop cognitive problems and at predicting how soon they would become noticeably impaired.
Next, the scientists paired the biomarkers data with demographic information, testing to see if sex, age, race, education and other factors could improve their predictions.
‘Sex, age and race all helped to predict who would develop cognitive impairment,’ Roe said. ‘Older participants, men and African Americans were more likely to become cognitively impaired than those who were younger, female and Caucasian.’
Roe described the findings as providing more evidence that scientists can detect Alzheimer’s disease years before memory loss and cognitive decline become apparent.
‘We can better predict future cognitive impairment when we combine biomarkers with patient characteristics,’ she said. ‘Knowing how accurate biomarkers are is important if we are going to some day be able to treat Alzheimer’s before symptoms and slow or prevent the disease.’
Clinical trials are already underway at Washington University and elsewhere to determine if treatments prior to symptoms can prevent or delay inherited forms of Alzheimer’s disease. Reliable biomarkers for Alzheimer’s should one day make it possible to test the most successful treatments in the much more common sporadic forms of Alzheimer’s. Washington University School of Medicine

Researchers from the RIKEN Center for Integrative Medical Sciences in Japan have identified the first gene to be associated with adolescent idiopathic scoliosis (also called AIS) across Asian and Caucasian populations. The gene is involved in the growth and development of the spine during childhood.
AIS is the most common pediatric skeletal disease, affecting approximately 2% of school-age children. The causes of scoliosis remain largely unknown and brace treatment and surgery are the only treatment options. However, many clinical and genetic studies suggest a contribution of genetic factors.
To understand the causes and development of scoliosis, Dr Ikuyo Kou, Dr Shiro Ikegawa and their team have tried to identify genes that are associated with a susceptibility to develop the condition.
By studying the genome of 1,819 Japanese individuals suffering from scoliosis and comparing it to 25,939 Japanese individuals, the team identified a gene associated with a susceptibility to develop scoliosis on chromosome 6. The association was replicated in Han Chinese and Caucasian populations.
The researchers show that the susceptibility gene, GPR126, is highly expressed in cartilage and that suppression of this gene leads to delayed growth and bone tissue formation in the developing spine. GPR126 is also known to play a role in human height and trunk length.
‘Our finding suggest the interesting possibility that GPR126 may affect both AIS susceptibility and height through abnormal spinal development and growth,’ explain the authors.
‘Further functional studies are necessary to elucidate how alterations in GPR126 increase the risk of AIS in humans,’ they conclude. Medical News Today

Researchers at the UCL Institute of Neurology together with international collaborators have identified a new gene, BICD2, which causes both dominant Congenital Spinal Muscular Atrophy and Hereditary Spastic Paraparesis. The team was led by Professor Mary Reilly.
Dominant Congenital Spinal Muscular Atrophy is a disorder of developing anterior horn cells and is characterised by lower limb predominance whereas Hereditary Spastic Paraparesis develops in childhood or adult life and is also a lower limb predominant disorder but of the corticospinal motor neurons.
The importance of this gene for motor nerves is underlined by the simultaneous publication of the same gene causing dominant Congenital Spinal Muscular Atrophy by two other groups.
The identification of the gene by exome sequencing and the subsequent functional work to study the pathogenesis of the disorder formed a major part of the PhD of Dr. Alex Rossor, a PhD student in the MRC Centre for Neuromuscular Diseases in the Institute of Neurology. UCL Institute of Neurology