Posts tagged science
Articles and news from the latest research reports.
Source: Medical Billing & Coding
Stanford researchers produce first complete computer model of an organism
A mammoth effort has produced a complete computational model of the bacterium Mycoplasma genitalium, opening the door for biological computer-aided design.
In a breakthrough effort for computational biology, the world’s first complete computer model of an organism has been completed, Stanford researchers reported last week in the journal Cell.
A team led by Markus Covert, assistant professor of bioengineering, used data from more than 900 scientific papers to account for every molecular interaction that takes place in the life cycle of Mycoplasma genitalium, the world’s smallest free-living bacterium.
By encompassing the entirety of an organism in silico, the paper fulfills a longstanding goal for the field. Not only does the model allow researchers to address questions that aren’t practical to examine otherwise, it represents a stepping-stone toward the use of computer-aided design in bioengineering and medicine.
"This achievement demonstrates a transforming approach to answering questions about fundamental biological processes," said James M. Anderson, director of the National Institutes of Health Division of Program Coordination, Planning and Strategic Initiatives. "Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and, ultimately, to inform new approaches for the diagnosis and treatment of disease."
The research was partially funded by an NIH Director’s Pioneer Award from the National Institutes of Health Common Fund.
Monkey manoeuvres reveal how the brain spurs actions
19 July 2012 by Nicola Guttridge
Whether a tree branch or a computer mouse is the target, reaching for objects is fundamental primate behaviour. Neurons in the brain prepare for such movements, and this neural activity can now be deciphered, allowing researchers to predict what movements will occur. This discovery could help us develop prosthetic limbs that can be controlled by thought alone.
What happens next? (Image: Gallo Images/Rex Features)
To find out what goes on in the brain when we reach for things, biomedical engineers Daniel Moran and Thomas Pearce at Washington University in St Louis, Missouri, trained two rhesus macaques to participate in a series of exercises. When the monkeys reached for items, electrodes measured the activity of neurons in their dorsal premotor cortex, a region of the brain that is involved in the perception of movement.
The monkeys were trained to reach for a virtual object on a screen to receive a reward. In some tasks the monkeys had to reach directly for an object, in others they had to reach around an obstacle to get to the target.
Impulsive grab
Moran and Pearce managed to identify the neural activity corresponding with several aspects of the planned movement, such as angle of reach, hand position and the final target location.
The findings could one day allow the design of prosthetic limbs that can be controlled with thought alone, which is “one of the reasons we did the study”, says Moran.
"The two subjects actually used different strategies to perform the task, and we were able to see this in their neural activity," Moran says. One monkey waited to receive all the information before reaching, but the other reached immediately, even though there was a good chance that an obstacle might appear and the reaching action would need to be rethought.
"If the decoding strategy is a robust finding, then this has wider consequences concerning mind-reading – particularly if we can get equivalent results for more complex strategic differences at higher cognitive levels," says Richard Cooper, a cognitive researcher at Birkbeck, University of London. "However, this is all very speculative."
Source: NewScientist
Brain satnav helps surgeons travel to a tumour
SATNAV is good at finding the easiest route to where you want to go. Now a version for the brain could allow a flexible probe to take the safest route to reach deep tissue. Together, the algorithm and probe could provide access to brain tumours that were previously deemed inoperable.
When surgeons want to take a biopsy from deep inside the brain, they face a problem - how to get there without damaging the brain tissue en route. Flexible needles are one solution. Ferdinando Rodriguez y Baena at Imperial College London and colleagues created such a probe in 2009, basing the design on the needle-like ovipositor that female wasps use to deposit eggs inside trees.
Just like the wasp’s ovipositor, the probe has a number of interlocking flexible shafts, each of which can slide independently of the others. The probe naturally sticks to the soft brain tissue, providing traction, which means that when one of the shafts slides further into the tissue the probe will flex. By controlling the relative movement of each shaft it is possible to send the probe snaking along a path through the tissue.
Rodriguez y Baena’s team has now begun to think about exactly which paths are best to take. “Some areas of the brain are more important than others and we needed a way to decide what route caused the least amount of damage to vital areas,” says team member Seong Young Ko at Chonnam National University in Gwangju, South Korea. “You would want to stay well away from major blood vessels and sensory areas, for example.”
The team has now developed an algorithm to direct the probe around these obstacles. It considers three factors: the distance from the scalp to the desired brain tissue, the proximity of the route to vital areas such as blood vessels or nerve bundles, and the accumulated risk along the way.
There is controversy over how to rate the importance of different parts of the brain, so the team tested the algorithm by giving arbitrary levels of importance to different areas. It revealed the path which should theoretically bring the least risk to a patient. Ko presented the algorithm at the BioRob 2012 conference in Rome, Italy, last month.
"The ability to take a curved path through the brain, selecting the most forgiving route to avoid critical regions, represents an intriguing breakthrough," says Katrina Firlik, a neurosurgeon in Greenwich, Connecticut, who was not involved in the research. "It could not only enhance safety but might even expand the surgical repertoire to include cases currently deemed inoperable."
That is the hope, says Ko. So far the probe has only been tested in animal tissue, but he says the goal is to use the algorithm to guide the safe implantation of electrodes deep in the brain and to improve the safety of taking biopsies from hard-to-reach tumours.
Why Facial Disfigurements Creep Us Out
Whether we realize it or not, most of us have a knee-jerk reaction when we see someone with a facial disfigurement, such as psoriasis, a cleft lip, or a birthmark. We may sit away from them on the bus, hesitate to shake their hand, or even give a barely masked look of revulsion. A new study suggests these disgust reactions stem from an ancient disease-avoidance system that normally prevents us from catching illnesses. Essentially, we treat facial disfigurements like infectious diseases.
Video games can be good for your health
Dr. Penelope McNulty, a neurophysiologist at Neuroscience Research Australia, will present new data that shows the Wii is an effective rehabilitation tool at an international conference of the Society of Electrophysiology and Kinesiology in Brisbane on 20 July.
Dr. McNulty’s data shows that an intensive, two-week training program based on the Wii can result in significant improvements in the way stroke patients are able to use their limbs, even for people that had a stroke many years ago.
“It was previously thought that the movement and function stroke patients had at the time they left hospital was the only recovery they would make,” says Dr. McNulty.
“But we have worked with people who have had strokes one month to 21 years ago, and excitingly, they all improve,” she added.
There are over 60,000 strokes in Australia each year and there is a crucial need to improve rehabilitation methods because this is the only method known to restore movement in stroke-affected limbs.
“The Wii is inexpensive, easy to use and, very importantly, fun. This type of rehabilitation motivates participants to actually complete their therapy, which is essential for maximum recovery,” Dr. McNulty says.
“Everyone notices improvements not just using the Wii, but in activities they do every day, such as opening a door or using a fork,” Dr. McNulty concluded.
Parkinson’s: Newly Discovered Antibody Could Facilitate Early Diagnosis
ScienceDaily (July 20, 2012) — Conditions such as Parkinson’s disease are a result of pathogenic changes to proteins. In the neurodegenerative condition of Parkinson’s disease, which is currently incurable, the alpha-synuclein protein changes and becomes pathological. Until now, there have not been any antibodies that could help to demonstrate the change in alpha-synuclein associated with the disease. An international team of experts led by Gabor G. Kovacs from the Clinical Institute of Neurology at the MedUni Vienna has now discovered a new antibody that actually possesses this ability.
"It opens up new possibilities for the development of a diagnostic test for Parkinsonism," says Kovacs, highlighting the importance of this discovery. "This new antibody will enable us to find the pathological conformation in bodily fluids such as blood or CSF." A clinical study involving around 200 patients is already underway, and the first definitive results are expected at the end of 2012. The tests being carried out in collaboration with the University Department of Neurology, led by Walter Pirker, are designed to determine the extent to which the new antibody can be used as an early diagnostic tool in order to understand the condition better and be able to treat it more effectively.
A step towards a blood test for Parkinson’s With Parkinsonism, the diseased form of alpha-synuclein, which has the same primary structure as the healthy form, undergoes an “abnormal fold.” Says Kovacs: “Until now, however, it was not possible to distinguish between the two.” The previous immunodiagnostic techniques only allowed the general presence of alpha-synuclein to be confirmed. The new, monoclonal antibody, however, which the researchers at the MedUni Vienna have developed in collaboration with the German biotech firm Roboscreen, is now able to detect a strategic part of the protein responsible for the structural changes. The results of the study have now been published in the journal Acta Neuropathologica.
Says Kovacs: “It is still not possible to say whether or not we will be able to diagnose Parkinson’s from a blood test, but this discovery certainly represents a major step in that direction.” Theoretically, it should be possible to diagnose Parkinson’s disease five to eight years before it develops.
In Austria, there are between 15,000 and 16,000 people living with Parkinson’s syndrome. Its frequency increases with age. As society becomes older, Parkinson’s disease, a degenerative condition of the brain, will become an increasingly widespread problem.
Source: Science Daily
Cell Research Opens New Avenues in Combating Neurodegenerative Diseases
ScienceDaily (July 20, 2012) — Scientists at the University of Manchester have uncovered how the internal mechanisms in nerve cells wire the brain. The findings open up new avenues in the investigation of neurodegenerative diseases by analysing the cellular processes underlying these conditions.
Illustration of spectraplakins in axonal growth organising microtubules. (Credit: Image courtesy of University of Manchester)
Dr Andreas Prokop and his team at the Faculty of Life Sciences have been studying the growth of axons, the thin cable-like extensions of nerve cells that wire the brain. If axons don’t develop properly this can lead to birth disorders, mental and physical impairments and the gradual decay of brain capacity during aging.
Axon growth is directed by the hand shaped growth cone which sits in the tip of the axon. It is well documented how growth cones perceive signals from the outside to follow pathways to specific targets, but very little is known about the internal machinery that dictates their behaviour.
Dr Prokop has been studying the key driver of growth cone movements, the cytoskeleton. The cytoskeleton helps to maintain a cell’s shape and is made up of the protein filaments, actin and microtubules. Microtubules are the key driving force of axon growth whilst actin helps to regulate the direction the axon grows.
Dr Prokop and his team used fruit flies to analyse how actin and microtubule proteins combine in the cytoskeleton to coordinate axon growth. They focussed on the multifunctional proteins called spectraplakins which are essential for axonal growth and have known roles in neurodegeneration and wound healing of the skin.
What the team demonstrate in this recent paper is that spectraplakins link microtubules to actin to help them extend in the direction the axon is growing. If this link is missing then microtubule networks show disorganised criss-crossed arrangements instead of parallel bundles and axon growth is hampered.
By understanding the molecular detail of these interactions the team made a second important finding. Spectraplakins collect not only at the tip of microtubules but also along the shaft, which helps to stabilise them and ensure they act as a stable structure within the axon.
This additional function of spectraplakins relates them to a class of microtubule-binding proteins including Tau. Tau is an important player in neurodegenerative diseases, such as Alzheimer’s, which is still little understood. In support of the author’s findings, another publication has just shown that the human spectraplakin, Dystonin, causes neurodegeneration when affected in its linkage to microtubules.
Talking about his research Dr Prokop said: “Understanding cytoskeletal machinery at the cell level is a holy grail of current cell research that will have powerful clinical applications. Thus, cytoskeleton is crucially involved in virtually all aspects of a cell’s life, including cell shape changes, cell division, cell movement, contacts and signalling between cells, and dynamic transport events within cells. Accordingly, the cytoskeleton lies at the root of many brain disorders. Therefore, deciphering the principles of cytoskeletal machinery during the fundamental process of axon growth will essentially help research into the causes of a broad spectrum of diseases. Spectraplakins like at the heart of this machinery and our research opens up new avenues for its investigation”
What Dr Prokop’s paper in the Journal of Neuroscience also demonstrates is the successful research technique using the fruit fly Drosophila. The team was able to replicate its findings regarding axon growth in mice which in turn means the findings can be translated to humans.
Dr Prokop points out fruit flies provide ideal means to make sense of these findings and essentially help to unravel the many mysteries of neurodegeneration.
Dr Prokop continues: “Understanding how spectraplakins perform their cellular functions has important implications for basic as well as biomedical research. Thus, besides their roles during axon growth, spectraplakins of mice and humans are clinically important for a number of conditions and processes including skin blistering, neuro-degeneration, wound healing, synapse formation and neuron migration during brain development. Understanding spectraplakins in one biological process will instruct research on the other clinically relevant roles of these proteins.”
Source: Science Daily
Music has big brain benefits compared to other leisure pursuits
Music rocks. Musical activity was found to preserve cognition, including memory, as you age, when comparing variability in cognitive outcomes of older adults active in musical instrumental and other leisure activities.
You won’t lose it if you don’t use it. A range of cognitive benefits including memory were sustained for musicians between the ages of 60-80 if they played for at least 10 years throughout their life, confirming the maintenance of advantages is not reliant on continued activity.
Start young. Timing of musical instrumental acquisition, before age nine, is important in optimizing cognitive benefits and was associated with enhanced verbal working memory functions.
It’s never too late, so keep at it. Sustained musical activity over the age of 60 was associated with other nonverbal cognitive benefits, and appeared to compensate for low educational attainment, which is possibly the greatest protection against age-related cognitive declines. This suggests that musical training should be considered an alternative form of education.
Anti-Tau Drug Improves Cognition, Decreases Tau Tangles in Alzheimer’s Disease Models
ScienceDaily (July 19, 2012) — While clinical trial results are being released regarding drugs intended to decrease amyloid production — thought to contribute to decline in Alzheimer’s disease — clinical trials of drugs targeting other disease proteins, such as tau, are in their initial phases.
Penn Medicine research presented July 19 at the 2012 Alzheimer’s Association International Conference (AAIC) shows that an anti-tau treatment called epithilone D (EpoD) was effective in preventing and intervening the progress of Alzheimer’s disease in animal models, improving neuron function and cognition, as well as decreasing tau pathology.
By targeting tau, the drug aims to stabilize microtubules, which help support and transport of essential nutrients and information between cells. When tau malfunctions, microtubules break and tau accumulates into tangles.
"This drug effectively hits a tau target by correcting tau loss of function, thereby stabilizing microtubules and offsetting the loss of tau due to its formation into neurofibrillary tangles in animal models, which suggests that this could be an important option to mediate tau function in Alzheimer’s and other tau-based neurodegenerative diseases," said John Trojanowski, MD, PhD, professor of Pathology and Laboratory Medicine in the Perelman School of Medicine at the University of Pennsylvania. "In addition to drugs targeting amyloid, which may not work in advanced Alzheimer’s disease, our hope is that this and other anti-tau drugs can be tested in people with Alzheimer’s disease to determine whether stabilizing microtubules damaged by malfunctioning tau protein may improve clinical and pathological outcomes."
The drug, identified through Penn’s Center for Neurodegenerative Disease Research (CNDR) Drug Discovery Program, was previously shown to prevent further neurological damage and improve cognitive performance in animal models*. The Penn research team includes senior investigator Bin Zhang, MD, and Kurt Brunden, PhD, director of Drug Discovery at CNDR.
Bristol-Myers Squibb, who developed and owns the rights to the drug, has started enrolling patients into a phase I clinical trial in people with mild Alzheimer’s disease.
Source: Science Daily