30 Kasım 2014 Pazar

Duality in the human genome

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Humans don’t like being alone, and their genes are no different. Together we are stronger, and the two versions of a gene – one from each parent – need each other.


Duality in the human genome



Every human being possesses a cis and trans mutations in a 60:40 ratio. In the cis configuration two mutations occur in one and the same genetic copy. The corresponding protein becomes incapacitated, but the second copy and the protein remain unaffected. In the trans configuration, however, both copies of the gene are mutated and produce two -damaged proteins. Photo Credit: © Art 4 Science



Scientists at the Max Planck Institute for Molecular Genetics in Berlin have analysed the genetic makeup of several hundred people and decoded the genetic information on the two sets of chromosomes separately. In this relatively small group alone they found millions of different gene forms. The results also show that genetic mutations do not occur randomly in the two parental chromosome sets and that they are distributed in the same ratio in everyone.


In 2001 scientists announced the successful decoding of the first human genome. Since then, thousands more have been sequenced. The price of a genetic analysis will soon fall below the 1,000 dollar mark. Given this rapid pace of development, it’s easy to forget that the technology used only reads a mixed product of genetic information. The analytical methods commonly employed do not take into account the fact that every person has two sets of genetic material. “So they are ignoring an essential property of the human genome. However, it’s important to know, for example, how mutations are distributed between the two chromosome sets,” says Margret Hoehe from the Max Planck Institute for Molecular Genetics, who carried out the study.


Hoehe and her team have developed molecular genetic and bioinformatic methods that make it possible to sequence the two sets of chromosomes in a human separately. The researchers decoded the maternal and paternal parts of the genome in 14 people and supplemented their analysis with the genetic material of 372 Europeans from the 1000 Genomes Project. “Fourteen people may not sound like a lot, but given the technical challenge, it is an unprecedented achievement,” says Hoehe.


The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word.


The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time. Moreover, the conventional view of individual mutations is no longer adequate. Instead, we have to consider the two gene forms and their combination of variants,” Hoehe explains. When analysing genomes, scientists should therefore examine each parental gene form separately, as well as the effects of both forms as a pair.


According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe. The 60:40 distribution ratio appears to be essential for survival. “This formula may help us to understand how gene variability occurs and how it affects gene function.”


Some of the many variants that alter the genome also have an effect at the protein level. The researchers have now identified a set of 4,000 genes that are altered by mutations so that their proteins occur especially frequently in two different forms in humans. These genes mainly control signal transmission between cells, the immune system and gene activity. This dual gene and protein arrangement has the advantage that it allows the activity of genes to be more flexibly adjusted and altered. By using the more favourable variant, the body is better able to adapt to changes in its own processes and to environmental conditions. If the duality of genes goes awry and the wrong protein form is used, this can trigger pathogenic mechanisms. This is probably why those 4,000 genes include many disease genes.


These findings will change the interpretation of genetic analyses and the prediction of diseases. Moreover, individualised medicine cannot ignore the “dual nature” of human genomes. “Our investigations at the protein level have shown that 96 percent of all genes have at least 5 to 20 different protein forms. This results in tremendous individual diversity in possible interactions between genes, and shows how daunting the challenge is to develop individually tailored therapies,” says Hoehe.


So far, researchers have estimated the risk of disease only by the presence or absence of mutations. However, there is evidence that in cancer, for example, the severity and course of the disease is determined by the wrong distribution of a mutation. The location of mutations therefore needs to be considered in the diagnosis, prediction and prevention of diseases in future.


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The above story is based on materials provided by Max Planck Institute for Molecular Genetics, Berlin.


Spinal cord has successfully been grown in a lab

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Researchers from the University of Dresden have used embryonic stem cells to grow an intact spinal cord in a petri dish, the team reported this week. It’s an enormous achievement in a field that has long viewed neural tissue as the ultimate challenge, and one which could give hope to millions of people suffering from spinal cord injuries.


stem cells



Photo credit: Eduardo Zattara (University of Maryland, College Park), Embryology 2012, Marine Biological Laboratory, Woods Hole, and Development. via Flickr.



The spinal cord, a cylinder about the width of a little finger which runs down the backbone and is the core component of the central nervous system, is a hugely complex structure. Creating spinal cord tissue from stem cells has eluded researchers for years.


Professor Elly Tanaka and her research group at the DFG Research Center for Regenerative Therapies Dresden – Cluster of Excellence at the TU Dresden (CRTD) demonstrated for the first time the in vitro growth of a piece of spinal cord in three dimensions.


For many years Elly Tanaka and her research group have been studying the regenerative potential of axolotls at the molecular level. The Mexican salamanders have the potential to regenerate their spinal cord and other organs to restore full functionality after injury. Mammals such as humans are not able to regenerate most organs. The restoration of the spinal cord in axolotl occurs in a three dimensional structure similar to an embryonic spinal cord. Due to their positions in the tissue, cells in the regenerated spinal cord know which function to perform in the restored tissue. “In this study we applied the knowledge gained about the regenerative potential in axolotls to a mammal, the mouse” explains Professor Elly Tanaka.


Single mouse embryonic stem cells embedded in a three-dimensional matrix and were grown in neural differentiation medium led to the clonal development of neuroepithelial cysts. These cysts settled in the midbrain and hindbrain along the neural axis. “Our goal, however, was to generate spinal cord in vitro,” says Dr. Andrea Meinhardt, a postdoc at the CRTD. “For this reason we added retinoic acid to the culture medium on the second day of the 3D cell culture.” The result not only caused the neural tissue to switch to spinal cord but also induced the formation of a local signaling center for forming all the different cell types of the spinal cord. “For the first time we could hereby reconstruct the structure of a typical embryonic neural tube in vitro,” said Andrea Meinhardt. „With this study we have moved a tiny step closer to turn the idea of constructing a three-dimensional piece of spinal cord for transplantation in humans into reality“ says Elly Tanaka.


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The above story is based on materials provided byCRTD/DFG-Research Center for Regenerative Therapies Dresden – Cluster of Excellence at the TU Dresden.


‘Chatty’ Cells Help Build the Brain

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Development of the cerebral cortex is influenced by genetic cues and communication between neurons and progenitors.


chatty cells



Fluorescence microscopy image of a mouse cortex during brain development. Blue cells are deep-layer neurons, green cells are Foxg1 active cells and red cells are upper-layer neurons. This image shows that the onset of Foxg1 activity instructs the production of both deep- and upper-layer neurons. Photo Credit K. Toma et al./Journal of Neuroscience.



The cerebral cortex, which controls higher processes such as perception, thought and cognition, is the most complex structure in the mammalian central nervous system. Although much is known about the intricate structure of this brain region, the processes governing its formation remain uncertain. Research led by Carina Hanashima from the RIKEN Center for Developmental Biology has now uncovered how feedback between cells, as well as molecular factors, helps shape cortical development during mouse embryogenesis.


The cortex is made up of layers of interconnecting cells that are produced in a particular order from progenitor cells. The relatively cell-sparse outer layer is formed first, then the dense deep layer, and finally the tightly packed upper layer. Hanashima and her colleagues were interested to discover exactly how the various layers form, so they created a mouse model that enabled them to control the expression of a particular protein, Foxg1, known to be involved in cortical development.


The Foxg1 gene, if switched on toward the end of embryogenesis after the outer layer of neurons has formed, triggers the production of deep-layer neurons, followed by upper-layer neurons. The researchers found that it does this by repressing the activity of another gene, called Tbr1, in the outer-layer neurons.


Genetics, however, is not the only factor that influences the development of this complicated laminar structure. In a separate experiment, the researchers let natural embryonic development run its course until the deep-layer neurons had formed, after which they selectively killed off these cells. At a point in time when the production of deep-layer cells would normally have ceased, it instead continued. The absence of the ‘production stop’ signal from deep-layer neurons caused the progenitor cells to continue to make deep-layer neurons. “Before this study, there was no evidence for any feedback between post-mitotic neurons and progenitors,” says Hanashima, “but we’ve shown that the two cell types do communicate.”


Extrinsic, cellular factors as well as intrinsic, genetic cues help to guide cortical development. This mechanism allows the developing brain to balance the various different cell types found in the neocortex: it gives the brain flexibility to adjust if too few of one cell type are produced. Although the numbers of cells and embryonic and gestational periods differ significantly between mice and humans, both species are endowed with almost identical genetic toolkits, and consequently the researchers think it is likely that the human neocortex is generated in much the same way.


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The above story is based on materials provided by RIKEN, Carina Hanashima.


Bioengineered Bacteria Ripen Fruit By Belching Ethylene

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The ruby red rows of tomatoes at the local grocery store don’t come off the vine in such a pretty state. Food producers pick fruits while unripe and later douse them with ethylene, a gas that plants naturally produce to trigger ripening. The ethylene used by food producers comes from cracking fossil fuels. As a green alternative, Cristina Del Bianco of the University of Trento, in Italy, and her team bioengineered Escherichia coli to produce ethylene to accelerate fruit ripening (ACS Synth. Biol. 2014, DOI: 10.1021/sb5000077).


fruit



Researchers grew cultures of ethylene-producing bacteria in flasks connected to jars containing unripe fruits such as cherry tomatoes, pears, apples, and bananas. The ethylene helped ripen the fruit. Photo Credit: Laboratory of Cristina Del Bianco



To program E. coli to make the gas, the scientists turned to another microbe called Pseudomonas syringae. This plant pathogen has an enzyme that converts 2-oxoglutarate, a citric acid cycle intermediate, to ethylene in a single step. The researchers inserted the gene into E. coli so that they could turn it on in the presence of the sugar arabinose. When they added arabinose to liquid cultures of the bacteria, ethylene levels in the flasks reached 100 ppm.


Next, the researchers grew the bacteria in flasks connected to jars filled with unripe cherry tomatoes, kiwis, or apples. After eight days, the fruits connected to flasks that received a dose of arabinose were significantly riper than those connected to bacterial cultures that didn’t get the sugar. The tomatoes were redder, the kiwis were softer, and the apples had less starch—a signature of ripening.


To make ethylene production easier for commercial applications, the team reengineered the bacteria so that they expressed the ethylene gene when exposed to blue light. The researchers detected 92 ppm of ethylene in a culture of these bacteria grown in blue light, whereas no ethylene was detected from bacteria grown in the dark.


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The above story is based on materials provided by American Chemical Society, Erika Gebel Berg.


29 Kasım 2014 Cumartesi

A hybrid vehicle that delivers DNA

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The new transport system for DNA vaccines could help treat HIV, malaria, HPV and other major illnesses


dna vehicle



University at Buffalo researchers, including Charles Jones, far right, a doctoral candidate in the Department of Chemical and Biological Engineering, are developing new technology to improve DNA vaccines.



A new hybrid vehicle is under development.Its performance isn’t measured by the distance it travels, but rather the delivery of its cargo: vaccines that contain genetically engineered DNA to fight HIV, cancer, influenza and other maladies.


Described recently in the Proceedings of the National Academy of Sciences, the technology is a biomedical advancement that could help unleash the potential of DNA vaccines, which despite two decades of research, have yet to make a significant impact in the treatment of major illnesses.


“The technology that we’re developing could help take immunization to the next level,” said Blaine A. Pfeifer, PhD, an associate professor in the Department of Chemical and Biological Engineering in the School of Engineering and Applied Sciences at the University at Buffalo.


Pfeifer, the study’s lead author, added: “By improving the delivery of DNA vaccines, we can potentially harness the human immune system in new ways to fight everything from the flu and herpes to HIV and cancer.”


Conventional vaccines, like those used to fight polio and smallpox, are typically composed of an agent that contains weakened or killed forms of the disease-causing microbe. The agent prompts the immune system to recognize the agent as foreign, destroy it, and keep a record of it so the immune system can more effectively fight it in the future.


While effective, some vaccines don’t last, others can revert to dangerous forms and some are costly and time-consuming to develop. Furthermore, no effective vaccines exist for cancer, malaria and others diseases that kill millions of people worldwide annually.


DNA vaccines could address these problems.


To create them, researchers analyze disease-causing sources, such as a pathogenic microbe. They then isolate copies of the microbe’s genes (usually one or two) responsible for the disease.


The genetically engineered DNA is injected into the body, whereupon being processed by the immune cells, directs the production and presentation of antigens which provoke an adaptive immune response capable of destroying the disease.


Essentially, the body’s own cells become vaccine-making factories that create the antigens necessary to stimulate the immune system, according to the National Institute of Allergy and Infectious Diseases.


In theory, DNA vaccines can generate broad immune responses; they are relatively inexpensive to create; and they can’t cause the disease because they don’t contain the source of the disease, only a few of its genes. Dozens of clinical trials involving DNA vaccines are underway. Most are investigating treatments for HIV and cancer, while others involve influenza, hepatitis B and C, HPV and malaria.


A problem limiting the effectiveness of some DNA vaccines, however, is that they do not sufficiently stimulate the immune system. Scientists say this is due, in part, to the inefficient delivery of the genes. For example, some travel to the wrong place while others get caught in intracellular traffic jams.


To address the problem, Pfeifer and his students collaborated with Anders Hakansson, PhD, formerly of the UB School of Medicine and Biomedical Sciences, and a senior co-author of the study.


The team combined two delivery vehicles – a bacterial cell and a synthetic polymer – to create a hybrid. Designed to target specific immune cells (antigen-presenting cells) and more efficiently deliver genes to the nucleus of those cells, the hybrid outperformed the two individual delivery vehicles when tested in a mouse model.


“The hybrid provided a synergistic boost in delivery effectiveness due to its dual nature,” said Charles H. Jones, a doctoral candidate in the Department of Chemical and Biological Engineering at UB and the study’s first author. “We also determined that it’s relatively inexpensive to create and flexible in terms of use. The results thus far are very encouraging.”


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The above story is based on materials provided by St. Michael’s Hospital.


28 Kasım 2014 Cuma

Nervous system may play bigger role in infections than previously known

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The nervous system may play a bigger role in infections and autoimmune diseases than previously known. If researchers can learn more about that role, it could provide insight into diagnosing and treating everything from the stomach flu to rheumatoid arthritis.


nerve


Researchers at St. Michael’s Hospital in Toronto, in conjunction with the Feinstein Institute for Medical Research in Manhasset, N.Y., reviewed the latest, most vigorous pre-clinical trials on this topic in a commentary published Thursday (Nov. 27) in the New England Journal of Medicine.


They noted that neurons of the peripheral nervous system – specialized nerve cells that transmit information throughout the body – are known to send information about local infections or inflammation to the central nervous system (the brain and spinal cord) so the CNS can co-ordinate the whole body response.


Dr. Benjamin Steinberg, a post-doctoral fellow and an anesthesiology resident at St. Michael’s, hypothesized that the neurons may be sending the CNS not just a general Danger Warning but specific information about whether the infection is caused by a virus or bacteria, the type of bacteria present or the nature of the auto-immune reaction.


Basic science researchers are now trying to decipher that “neural code” of information being sent by neurons.


“The blue sky idea is that if we know the language and can read the code, in theory we can engineer or write our own,” said Dr. Steinberg, writing with coauthors Dr. Arthur Slutsky, vice-president of research at St. Michael’s and Dr. Kevin Tracey, president of the Feinstein Institute.


Since those messages are being sent from neurons to the CNS in real time, knowing what they’re saying could speed diagnoses or prognostication, which would be especially important in pandemics or outbreaks of particularly contagious or deadly diseases, such as flu, Ebola or SARS. The current method for confirming infections is to test body fluids or tissues, sometimes using invasive techniques, a process that can take hours, days or even longer. Moreover, Dr Steinberg said researchers might even be able to tell how severe an infection is and how the illness is expected to progress without treatment.


“Timely diagnosis and intervention are essential to minimize deaths and complications,” said Dr. Steinberg. “If the neurons are reading this information from an infection in the blood or the liver and we can interrogate the nervous system, we can make a diagnosis in real time. For example, we could perhaps tell quickly whether someone has the flu virus or bacterial pneumonia, which would determine whether antibiotics would be appropriate. At the extreme, a patient in septic shock requires prompt administration of antibiotic agents since each hour of delay is associated with a 7.6 per cent increase in mortality, but physicians do not always know what bacterium they need to target. An inappropriately chosen antibiotic can have serious ramifications for patient well-being.”


It’s already possible to intercept and change some messages being sent to the CNS using bioelectric therapy. When injured, pain receptors send messages to the CNS that are registered as pain. Bioelectric therapy relieves pain by interrupting pain signals before they reach the brain. It also prompts the body to produce endorphins, which help to relieve pain.


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The above story is based on materials provided by St. Michael’s Hospital.


Scientists discover treatment breakthrough for advanced bladder cancer

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Scientists from Queen Mary University of London have made a breakthrough in developing a new therapy for advanced bladder cancer – for which there have been no major treatment advances in the past 30 years.


Scientists discover treatment breakthrough for advanced bladder cancer


Published yesterday in Nature, the study examined an antibody (MPDL3280A) which blocks a protein (PD-L1) thought to help cancer cells evade immune detection.


In a phase one, multi-centre international clinical trial, 68 patients with advanced bladder cancer (who had failed all other standard treatments such as chemotherapy) received MPDL3280A, a cancer immunotherapy medicine being developed by Roche. In addition, patients were all tested for the protein PD-L1 and around 30 were identified as having PD-L1 positive tumours.


After six weeks of treatment, 43 per cent of PD-L1-positive patients found their tumour had shrunk. This rose to 52 per cent after 12 weeks of follow up. In two of these patients (7 per cent) radiological imaging found no evidence of the cancer at all following the treatment. Among PD-L1 negative patients, 11 percent responded positively to treatment too.


Patients who had a positive response to treatment found the benefits were prolonged, and safety results were also encouraging, with fatigue and loss of appetite most commonly reported as side effects.


The early results of this trial are so promising, the MPDL3280A antibody drug has been given breakthrough therapy designation status by the U.S. FDA.


Dr Tom Powles, Lead Author and Consultant Medical Oncologist, Barts Cancer Institute, Queen Mary University of London, comments: “This study is a hugely exciting step forward in the search for alternative advanced bladder cancer treatment. For decades chemotherapy has been the only option, with a poor outcome and many patients too ill to cope with it. Not only has this investigational drug had a striking response rate, we can target this therapy for patients by screening specific protein PD-L1.


“We now need larger trials to confirm our findings, and as this drug has been given breakthrough designation status by the FDA, we hope to fast track this process so we can begin to give hope to the thousands of people affected by advanced bladder cancer each year.”


Bladder cancer is the 7th most common cancer in the UK and around 10% of diagnoses are advanced (meaning the cancer has already spread to another part of the body). This makes it very difficult to treat, with chemotherapy the only option. On average patients live for 12 – 18 months following diagnosis, with many choosing to forgo chemotherapy due to its toxicity and limited survival benefit.


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The above story is based on materials provided by Queen Mary, University of London.


Copper on the Brain at Rest

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BIOENGINEER.ORG http://bioengineer.org/copper-on-the-brain-at-rest/



In recent years it has been established that copper plays an essential role in the health of the human brain. Improper copper oxidation has been linked to several neurological disorders including Alzheimer’s, Parkinson’s, Menkes’ and Wilson’s. Copper has also been identified as a critical ingredient in the enzymes that activate the brain’s neurotransmitters in response to stimuli. Now a new study by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) has shown that proper copper levels are also essential to the health of the brain at rest.


Chris-Chang



Chris Chang is a faculty chemist with Berkeley Lab and UC Berkeley, and an HHMI investigator. Photo Credit: Roy Kaltschmidt



“Using new molecular imaging techniques, we’ve identified copper as a dynamic modulator of spontaneous activity of developing neural circuits, which is the baseline activity of neurons without active stimuli, kind of like when you sleep or daydream, that allows circuits to rest and adapt,” says Chris Chang, a faculty chemist with Berkeley Lab’s Chemical Sciences Division who led this study.


“Traditionally, copper has been regarded as a static metabolic cofactor that must be buried within enzymes to protect against the generation of reactive oxygen species and subsequent free radical damage. We’ve shown that dynamic and loosely bound pools of copper can also modulate neural activity and are essential for the normal development of synapses and circuits.”


In recent years it has been established that copper plays an essential role in the health of the human brain. Improper copper oxidation has been linked to several neurological disorders including Alzheimer’s, Parkinson’s, Menkes’ and Wilson’s. Copper has also been identified as a critical ingredient in the enzymes that activate the brain’s neurotransmitters in response to stimuli. Now a new study by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) has shown that proper copper levels are also essential to the health of the brain at rest.


“Using new molecular imaging techniques, we’ve identified copper as a dynamic modulator of spontaneous activity of developing neural circuits, which is the baseline activity of neurons without active stimuli, kind of like when you sleep or daydream, that allows circuits to rest and adapt,” says Chris Chang, a faculty chemist with Berkeley Lab’s Chemical Sciences Division who led this study. “Traditionally, copper has been regarded as a static metabolic cofactor that must be buried within enzymes to protect against the generation of reactive oxygen species and subsequent free radical damage. We’ve shown that dynamic and loosely bound pools of copper can also modulate neural activity and are essential for the normal development of synapses and circuits.”


Figure 3



Two-photon imaging of CF3 shows that the addition of acute BCS dosages also reduces labile copper pools in retinal neurons. Photo Credit:Image courtesy of DOE/Lawrence Berkeley National Laboratory



Figure 3



Two-photon imaging of CF3 shows that the addition of acute BCS dosages also reduces labile copper pools in retinal neurons.



For this latest study, Chang and his group developed a fluorescent probe called Copper Fluor-3 (CF3) that can be used for one- and two-photon imaging of copper ions. This new probe allowed them to explore the potential contributions to cell signaling of loosely bound forms of copper in hippocampal neurons and retinal tissue.


“CF3 is a more hydrophilic probe compared to others we have made, so it gives more even staining and is suitable for both cells and tissue,” Chang says. “It allows us to utilize both confocal and two-photon imaging methods when we use it along with a matching control dye (Ctrl-CF3) that lacks sensitivity to copper.”


With the combination of CF3 and Ctrl-CF3, Chang and his group showed that neurons and neural tissue maintain stores of loosely bound copper that can be attenuated by chelation to create what is called a “labile copper pool.” Targeted disruption of these labile copper pools by acute chelation or genetic knockdown of the copper ion channel known as CTR1 (for copper transporter 1) alters spontaneous neural activity in developing hippocampal and retinal circuits.


“We demonstrated that the addition of the copper chelator bathocuproine disulfonate (BCS) modulates copper signaling which translates into modulation of neural activity,” Chang says. “Acute copper chelation as a result of additional BCS in dissociated hippocampal cultures and intact developing retinal tissue removed the copper which resulted in too much spontaneous activity.”


The results of this study suggest that the mismanagement of copper in the brain that has been linked to Wilson’s, Alzheimer’s and other neurological disorders can also contribute to misregulation of signaling in cell−to-cell communications.


“Our results hold therapeutic implications in that whether a patient needs copper supplements or copper chelators depends on how much copper is present and where in the brain it is located,” Chang says. “These findings also highlight the continuing need to develop molecular imaging probes as pilot screening tools to help uncover unique and unexplored metal biology in living systems.”


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The above story is based on materials provided by DOE/Lawrence Berkeley National Laboratory.


27 Kasım 2014 Perşembe

The future of fake meat

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BIOENGINEER.ORG http://bioengineer.org/the-future-of-fake-meat/



Alastair Gee: “In the future, how will we define meat?”


the



Featured illustration by Emily Pidgeon/TED.



At home one night earlier this month, I prepared a salad with simulated chicken made from pea and soy proteins. Later I had some cheese derived from almond milk, which I came across, in a testament to its verisimilitude, next to the dairy camemberts and bries at Whole Foods, rather than shelved with the vegan products. On offer nearby was a mayonnaise also based on pea protein. Soon, these products could be joined by two others in development: a milk intended to be produced in part by yeast, and chips made of meat grown in a medium. In thinking about these items, it was sometimes difficult for me to determine the extent to which they share in the essential nature of the foods they emulate. What is the quotient of cheeseness in the nut cheese, or of milkness in the yeast milk? And, for that matter, how should that essence be defined in the first place? At one point the foods involved — chicken, pea, milk, almond — struck me as merely variations on some fundamental substrate of nutrients, and the names became a hazy and untethered assortment of signifiers.



AT ONE POINT THE FOODS INVOLVED — CHICKEN, PEA, MILK, ALMOND — STRUCK ME AS MERELY VARIATIONS ON SOME FUNDAMENTAL SUBSTRATE OF NUTRIENTS.



Recently there has been growing interest in Silicon Valley and beyond in creating consumer foods that incorporate protein-rich replacements for farm-animal products like meat, dairy foods and eggs. It is a niche already occupied by tofu and soy, but some of the new companies disavow any similarities to them and are encouraging a semantic shift. They are not simply alternatives to animal foods, they say. They are analogs of them, or even new kinds of them. The website of one company, Beyond Meat, puts it like this: “What if you define meat by what it is — amino acids, fats, carbs, minerals, and water — versus where it is from (i.e cows, chickens, pigs)? What you’d have is meat for the future. Meat from plants.” In blurring categories like this, however, questions about marketing abound.



DEMAND FOR MEAT, PARTICULARLY IN ASIA’S BURGEONING MIDDLE-CLASSES, IS EXPECTED TO SOAR.



With the world’s population expected to climb to approach 10 billion by 2050, demand for meat, particularly in Asia’s burgeoning middle classes, is predicted to soar. Meanwhile, the U.N. has reported that raising cattle contributes more greenhouse gases to the atmosphere than does transportation, and that animal products are in general more carbon-intensive than plant-based options. The new food companies often tout their earth-friendly credentials — but they also represent the latest salvo in a lengthy discourse about the human race’s ability to provide for itself as it grows, which Warren Belasco, an American studies professor at the University of Maryland, Baltimore County, ably describes in Meals to Come.


Fears of a food crunch have loomed for centuries. In 1798, Thomas Malthus suggested that population growth would be checked by our capacity to produce food. Since then, various experts have prophesied an overload of the planet’s carrying capacity. A 1923 book by Harvard plant geneticist Edward M. East predicted that the planet was less than a century away from “saturation,” and that the year 2000 would find “a seething mass of discontented humanity struggling for mere existence.”



THE “CORNUCOPIAN” STRAIN OF THINKING HAS ITS ROOTS IN THE ENLIGHTENMENT.



At the same time there has long been a “cornucopian” strain of thinking, which Belasco traces to the Enlightenment, with its totems of progress and science. In this view, bountiful new means of food production will always be found to avert a Malthusian check. Writing just before Malthus, the philosopher Nicolas de Condorcet argued that even if there was some limit to population, there was nothing preventing “manufacturing animal and vegetable substances artificially.”


In the 20th century there were rich veins of optimistic, occasionally outlandish, ideas for food innovations. In 1928, the president of the American Chemical Society proclaimed that “thirty men working in a factory the size of a city block can produce in the form of yeast as much food as 1,000 men tilling 57,000 acres.” Winston Churchill imagined rearing chicken parts — breasts or wings — instead of whole animals. A 1949 book called The Coming Age of Wood touted yeast cultured in fermented sawdust. Some of the most grandiose hypothesizing in the 1940s and 1950s involved turning algae into a major food source. Collier’s magazine ran a story that envisioned enormous assemblages of transparent pipes in sunny seaside locations, such as the Gulf of Mexico or the Sea of Galilee. Algae would grow inside them, taking the form of butter or animal fodder.



WINSTON CHURCHILL IMAGINED REARING CHICKEN PARTS — BREASTS OR WINGS — INSTEAD OF WHOLE ANIMALS.



It is worth noting that many actual technological upheavals in the modern food industry have been of a different variety, often to do with preservation and storage. Iceberg lettuce became “the first industrial vegetable” in the early 20th century, says Gabriella Petrick, an associate professor in the department of nutrition and food studies at George Mason University, thanks partly to ice-producing facilities, which meant the lettuce could be kept cold, transported across the country from California and consumed out of season in its destinations. (Britain’s Royal Society named refrigeration as the most important food innovation in history.) In another development, canned goods were the first mass-produced foods, notes Petrick.


Today the question is whether the companies advocating the replacement of animals in the food chain will trigger an upheaval on the scale of refrigeration or canning, or if it is a shift only of interest to a limited segment – vegans, perhaps, and the health-conscious. The foods may win some popularity based on the idea that they are better for the environment, as they necessitate fewer greenhouse-gas emissions. They appeal to our sense of logic. But then, consider bugs. As University of the Pacific food historian Ken Albala notes, “there’s always been this idea that we should eat insects,” which are considered a more eco-friendly source of protein. “But we can’t get over it,” he says, meaning our squeamishness.



“IT MIGHT BE GOOD FOR THE ENVIRONMENT AND GOOD FOR ANIMALS, BUT IF IT TASTES BAD IT’S NOT GOING TO BE A SUCCESS.”



Our food decisions are not based purely on intellectual reasoning; for instance, many of us consume meat even though it’s clear most animals were raised in factory settings and didn’t have the best of lives. “If you’re going to come up with a food product, the subtitle might be that it’s good for the environment and good for animals, but if it tastes bad it’s not going to be a success,” says Andras Forgacs, a co-founder of Modern Meadow, which is working on culturing meat, as well as leather.


The appeal of these products may also depend on their appearance. Forgacs says he does not intend to produce items that mimic the look of existing meat forms — steak or mince — as this may raise expectations that cannot be satisfied. “You risk falling into this uncanny valley, where it’s not 100 percent like meat. It might be 98 percent like meat, but the 2 percent gap at the end is sufficient to make people feel like it’s not great.” He is focusing on novel incarnations, like chips containing cultured meat.


By contrast, Ethan Brown, the CEO and founder of Beyond Meat, which makes substitutes for chicken strips and ground beef from vegetable proteins, holds that traditional looks are a selling point. “I’ve played with ideas like: it could be just a square piece of a thing that looked like tofu but had all the nutritional elements of salmon, and had a fish stamped on it. It just communicates that this is a healthier version of something,” he muses. “But I think because of the familiarity that people have with animal protein consumption, it’s important to deliver it in a form that they’re used to.”


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The above story is based on materials provided by Ted Ideas.


26 Kasım 2014 Çarşamba

Two-Cell Mouse Embryos Talk About Their Future

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BIOENGINEER.ORG http://bioengineer.org/two-cell-mouse-embryos-talk-about-their-future/



Bioengineers at the University of California, San Diego have discovered that mouse embryos are contemplating their cellular fates in the earliest stages after fertilization when the embryo has only two to four cells, a discovery that could upend the scientific consensus about when embryonic cells begin differentiating into cell types.Their research, which used single-cell RNA sequencing to look at every gene in the mouse genome, was published recently in the journal Genome Research. In addition, this group published a paper on analysis of ”time-course”single-cell data which is taken at precise stages of embryonic development in the journal of Proceedings of the National Academy of Sciences.


ms2



The research team used single-cell RNA-sequencing to measure every gene in the mouse genome at multiple stages of development to find differences in gene expression at precise stages. Photo Credit: Art by Victor O. Leshyk provided courtesy



“Until recently, we haven’t had the technology to look at cells this closely,” said Sheng Zhong, a bioengineering professor at UC San Diego Jacobs School of Engineering, who led the research. “Using single-cell RNA-sequencing, we were able to measure every gene in the mouse genome at multiple stages of development to find differences in gene expression at precise stages.”


The findings reveal cellular activity that could provide insight into where normal developmental processes break down, leading to early miscarriages and birth defects.


The researchers discovered that a handful of genes are clearly signaling to each other at the two-cell and four-cell stage, which happens within days after an egg has been fertilized by sperm and before the embryo has implanted into the uterus. Among the identified genes are several genes belonging to the WNT signaling pathway, well-known for their role in cell-cell communications.


The prevailing view until now has been that mammalian embryos start differentiating into cell types after they have proliferated into large enough numbers to form subgroups. According to the co-authors Fernando Biase and Xiaoyi Cao, when the first cell fate decision is made is an open question. The first major task for an embryo is to decide which cells will begin forming the fetus, and which will form the placenta.


The research was funded by the National Institutes of Health (DP2OD007417) and the March of Dimes Foundation. The publications are “Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing”, Genome Research, November 2014 and “Time-variant clustering model for understanding cell fate decisions”, PNAS, November 2014.


Zhong’s research in the field of systems or network biology applies engineering principals to understand how biological systems function. For example, they developed analytical methods to predict personal phenotypes, which refer to the physical description of an individual ranging from eye and hair color to health and disposition, using an individual’s personal genome and epigenome. Epigenome refers to the chemical compounds in DNA that regulate gene expression and vary from person to person. Predicting phenotypes with genome and epigenome is an emerging area of research in the field of personalized medicine that scientists believe could provide new ways to predict and treat genetic disorders.


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The above story is based on materials provided by University of California – San Diego.


24 Kasım 2014 Pazartesi

Large biological circuits

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BIOENGINEER.ORG http://bioengineer.org/large-biological-circuits/



Researchers have made great progress in recent years in the design and creation of biological circuits — systems that, like electronic circuits, can take a number of different inputs and deliver a particular kind of output. But while individual components of such biological circuits can have precise and predictable responses, those outcomes become less predictable as more such elements are combined.


boo



An innovation from MIT could allow many biological components to be connected to produce predictable effects. Photo Credit: Illustration: Christine Daniloff/MIT (yeast cell images from National Institutes of Health)



A team of researchers at MIT has now come up with a way of greatly reducing that unpredictability, introducing a device that could ultimately allow such circuits to behave nearly as predictably as their electronic counterparts. The findings are published this week in the journal Nature Biotechnology, in a paper by associate professor of mechanical engineering Domitilla Del Vecchio and professor of biological engineering Ron Weiss.


The lead author of the paper is Deepak Mishra, an MIT graduate student in biological engineering. Other authors include recent master’s students Phillip Rivera in mechanical engineering and Allen Lin in electrical engineering and computer science.


There are many potential uses for such synthetic biological circuits, Del Vecchio and Weiss explain. “One specific one we’re working on is biosensing — cells that can detect specific molecules in the environment and produce a specific output in response,” Del Vecchio says. One example: cells that could detect markers that indicate the presence of cancer cells, and then trigger the release of molecules targeted to kill those cells.


It is important for such circuits to be able to discriminate accurately between cancerous and noncancerous cells, so they don’t unleash their killing power in the wrong places, Weiss says. To do that, robust information-processing circuits created from biological elements within a cell become “highly critical,” Weiss says.


To date, that kind of robust predictability has not been feasible, in part because of feedback effects when multiple stages of biological circuitry are introduced. The problem arises because unlike in electronic circuits, where one component is physically connected to the next by wires that ensure information is always flowing in a particular direction, biological circuits are made up of components that are all floating around together in the complex fluid environment of a cell’s interior.


Information flow is driven by the chemical interactions of the individual components, which ideally should affect only other specific components. But in practice, attempts to create such biological linkages have often produced results that differed from expectations.


“If you put the circuit together and you expect answer ‘X,’ and instead you get answer ‘Y,’ that could be highly problematical,” Del Vecchio says.


The device the team produced to address that problem is called a load driver, and its effect is similar to that of load drivers used in electronic circuits: It provides a kind of buffer between the signal and the output, preventing the effects of the signaling from backing up through the system and causing delays in outputs.


While this is relatively early-stage research that could take years to reach commercial application, the concept could have a wide variety of applications, the researchers say. For example, it could lead to synthetic biological circuits that constantly measure glucose levels in the blood of diabetic patients, automatically triggering the release of insulin when it is needed.


The addition of this load driver to the arsenal of components available to those designing biological circuits, Del Vecchio says, “could escalate the complexity of circuits you could design,” opening up new possible applications while ensuring that their operation is “robust and predictable.”


James Collins, a professor of biomedical engineering at Boston University who was not associated with this research, says, “Efforts in synthetic biology to create complex gene circuits are often hindered by unanticipated or uncharacterized interactions between submodules of the circuits. These interactions alter the input-output characteristics of the submodules, leading to undesirable circuit behavior.”


But now, Collins says, “Del Vecchio and Weiss have made a major advance for the field by creating a genetic device that can account for and correct for such interactions, leading to more predictable circuit behavior.”


The research was supported by an Eni-MIT Energy Research Fellowship, the National Science Foundation, the U.S. Army Research Office, the U.S. Air Force Office of Scientific Research, and the National Institutes of Health.


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The above story is based on materials provided by Massachusetts Institute of Technology.


‘Huge breakthrough’ in understanding how the immune system recognises cancer

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BIOENGINEER.ORG http://bioengineer.org/huge-breakthrough-in-understanding-how-the-immune-system-recognises-cancer/



US researchers have revealed the identity of molecules on the surface of cancer cells which allow the body’s immune system to identify and destroy them. The research could lead to a new generation of immunotherapies that are far more effective than those currently in use, that could target a range of cancers.


Huge breakthrough in understanding how the immune system recognises cancer


This discovery is big, big news for immunotherapy researchers – Dr Sergio Quezada, Cancer Research UK. “This is a huge breakthrough,” said Cancer Research UK’s Dr Sergio Quezada, who works at UCL in London and was not involved in the research.


“The researchers were looking for ‘signatures’ on the surface of cancer cells associated with response to current immunotherapies, but their findings go further than that. They’ve actually discovered molecular motifs that will inform the development of the next generation of therapies,” he added.


The researchers, led by a team at the Memorial Sloan Kettering Cancer Centre in New York, analysed cancer DNA from 64 melanoma patients who had been treated with an immunotherapy drug called ipilimumab, half of whom had responded to the drug.


Ipilimumab works by switching on the body’s immune system to attack their cancer, but – for unknown reasons – it only works effectively in a minority of patients.


“We’ve been using a drug that empirically was found to be quite effective, and yet we didn’t have a detailed understanding of how it was working in people,” said Memorial Sloan Kettering’s Dr Jedd Wolchok.


Having analysed the patients’ cancer DNA, the researchers used sophisticated software to look for genetic mutations in the cancer cells that could predict whether patients had, or hadn’t, responded to the drug.


In doing so, they uncovered a series of genetic mutations in some of the patients that caused the cancer cells to produce short stretches of protein molecules, called peptide antigens, that make cancerous cells visible to immune response.


Tantalisingly, it appears that these mutations cause the antigens to mimic small parts of proteins produced by bacteria and viruses, explaining why they are so effective at triggering the immune response – although the researchers say more research will be needed to confirm this.


The discovery is “big, big news” for immunotherapy researchers says Cancer Research UK’s Dr Quezada. “This is the first time we’ve had an idea of what the immune system actually ‘sees’ on a tumour. Until now, it’s been hot topic of debate,” he said.


More immediately, the findings could be used to predict which patients should be offered ipilimumab, which costs nearly £77,000 for a course of treatment.


“For the first time, it might be feasible to develop a reliable diagnostic test to help guide treatment decisions by predicting who will respond,” said Dr Timothy Chan, who lead the research team.


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The above story is based on materials provided by University of Cambridge.


23 Kasım 2014 Pazar

Imagination, reality flow in opposite directions in the brain

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BIOENGINEER.ORG http://bioengineer.org/imagination-reality-flow-in-opposite-directions-in-the-brain/



As real as that daydream may seem, its path through your brain runs opposite reality. Aiming to discern discrete neural circuits, researchers at the University of Wisconsin-Madison have tracked electrical activity in the brains of people who alternately imagined scenes or watched videos.


Imagination



Electrical and computer engineering Professor Barry Van Veen wears an electrode net used to monitor brain activity via EEG signals. His research could help untangle what happens in the brain during sleep and dreaming. Photo Credit: Nick Berard



“A really important problem in brain research is understanding how different parts of the brain are functionally connected. What areas are interacting? What is the direction of communication?” says Barry Van Veen, a UW-Madison professor of electrical and computer engineering. “We know that the brain does not function as a set of independent areas, but as a network of specialized areas that collaborate.”


Van Veen, along with Giulio Tononi, a UW-Madison psychiatry professor and neuroscientist, Daniela Dentico, a scientist at UW-Madison’s Waisman Center, and collaborators from the University of Liege in Belgium, published results recently in the journal NeuroImage. Their work could lead to the development of new tools to help Tononi untangle what happens in the brain during sleep and dreaming, while Van Veen hopes to apply the study’s new methods to understand how the brain uses networks to encode short-term memory.


During imagination, the researchers found an increase in the flow of information from the parietal lobe of the brain to the occipital lobe — from a higher-order region that combines inputs from several of the senses out to a lower-order region.


In contrast, visual information taken in by the eyes tends to flow from the occipital lobe — which makes up much of the brain’s visual cortex — “up” to the parietal lobe.


“There seems to be a lot in our brains and animal brains that is directional, that neural signals move in a particular direction, then stop, and start somewhere else,” says. “I think this is really a new theme that had not been explored.”


The researchers approached the study as an opportunity to test the power of electroencephalography (EEG) — which uses sensors on the scalp to measure underlying electrical activity — to discriminate between different parts of the brain’s network.


Brains are rarely quiet, though, and EEG tends to record plenty of activity not necessarily related to a particular process researchers want to study.


To zero in on a set of target circuits, the researchers asked their subjects to watch short video clips before

trying to replay the action from memory in their heads. Others were asked to imagine traveling on a magic bicycle — focusing on the details of shapes, colors and textures — before watching a short video of silent nature scenes.

Using an algorithm Van Veen developed to parse the detailed EEG data, the researchers were able to compile strong evidence of the directional flow of information.


“We were very interested in seeing if our signal-processing methods were sensitive enough to discriminate between these conditions,” says Van Veen, whose work is supported by the National Institute of Biomedical Imaging and Bioengineering. “These types of demonstrations are important for gaining confidence in new tools.”


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The above story is based on materials provided by University of Wisconsin-Madison.


22 Kasım 2014 Cumartesi

A lab the size of a postage stamp

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BIOENGINEER.ORG http://bioengineer.org/a-lab-the-size-of-a-postage-stamp/



Traditional lab tests for disease diagnosis can be too expensive and cumbersome for the regions most in need. George Whitesides’ ingenious answer is a foolproof tool that can be manufactured at virtually zero cost.



The problem that I want to talk with you about is really the problem of: How does one supply healthcare in a world in which cost is everything? How do you do that? And the basic paradigm we want to suggest to you, I want to suggest to you, is one in which you say that in order to treat disease you have to first know what you’re treating — that’s diagnostics — and then you have to do something.


So, the program that we’re involved in is something which we call Diagnostics for All, or zero-cost diagnostics. How do you provide medically relevant information at as close as possible to zero cost? How do you do it? Let me just give you two examples. The rigors of military medicine are not so dissimilar from the third world — poor resources, a rigorous environment, a series of problems in lightweight, and things of this kind — and also not so different from the home healthcare and diagnostic system world.


So, the technology that I want to talk about is for the third world, for the developing world, but it has, I think, much broader application, because information is so important in the healthcare system. So, you see two examples here. One is a lab that is actually a fairly high-end laboratory in Africa. The second is basically an entrepreneur who is set up and doing who-knows-what in a table in a market. I don’t know what kind of healthcare is delivered there. But it’s not really what is probably most efficient.


What is our approach? And the way in which one typically approaches a problem of lowering cost, starting from the perspective of the United States, is to take our solution, and then to try to cut cost out of it. No matter how you do that, you’re not going to start with a 100,000-dollar instrument and bring it down to no-cost. It isn’t going to work.


So, the approach that we took was the other way around. To ask, “What is the cheapest possible stuff that you could make a diagnostic system out of, and get useful information, add function?” And what we’ve chosen is paper. What you see here is a prototypic device. It’s about a centimeter on the side. It’s about the size of a fingernail. The lines around the edges are a polymer. It’s made of paper and paper, of course, wicks fluid, as you know, paper, cloth — drop wine on the tablecloth, and the wine wicks all over everything. Put it on your shirt, it ruins the shirt. That’s what a hydrophilic surface does.


So, in this device the idea is that you drip the bottom end of it in a drop of, in this case, urine. The fluid wicks its way into those chambers at the top. The brown color indicates the amount of glucose in the urine, the blue color indicates the amount of protein in the urine. And the combination of those two is a first order shot at a number of useful things that you want. So, this is an example of a device made from a simple piece of paper.


Now, how simple can you make the production? Why do we choose paper? There’s an example of the same thing on a finger, showing you basically what it looks like. One reason for using paper is that it’s everywhere. We have made these kinds of devices using napkins and toilet paper and wraps, and all kinds of stuff.


So, the production capability is there. The second is, you can put lots and lots of tests in a very small place. I’ll show you in a moment that the stack of paper there would probably hold something like 100,000 tests, something of that kind.


And then finally, a point that you don’t think of so much in developed world medicine: it eliminates sharps. And what sharps means is needles, things that stick. If you’ve taken a sample of someone’s blood and the someone might have hepatitis C, you don’t want to make a mistake and stick it in you. It just — you don’t want to do that. So, how do you dispose of that? It’s a problem everywhere. And here you simply burn it. So, it’s a sort of a practical approach to starting on things.


Now, you say, “If paper is a good idea, other people have surely thought of it.” And the answer is, of course, yes. Those half of you, roughly, who are women, at some point may have had a pregnancy test. And the most common of these is in a device that looks like the thing on the left. It’s something called a lateral flow immunoassay. In that particular test, urine either, containing a hormone called HCG, does or does not flow across a piece of paper. And there are two bars. One bar indicates that the test is working, and if the second bar shows up, you’re pregnant.


This is a terrific kind of test in a binary world, and the nice thing about pregnancy is either you are pregnant or you’re not pregnant. You’re not partially pregnant or thinking about being pregnant or something of that sort. So, it works very well there, but it doesn’t work very well when you need more quantitative information.


There are also dipsticks, but if you look at the dipsticks, they’re for another kind of urine analysis. There are an awful lot of colors and things like that. What do you actually do about that in a difficult circumstance? So, the approach that we started with is to ask: Is it really practical to make things of this sort? And that problem is now, in a purely engineering way, solved. And the procedure that we have is simply to start with paper. You run it through a new kind of printer called a wax printer. The wax printer does what looks like printing. It is printing. You put that on, you warm it a little bit, the wax prints through so it absorbs into the paper, and you end up with the device that you want.


The printers cost 800 bucks now. They’ll make, we estimate that if you were to run them 24 hours a day they’d make about 10 million tests a year. So, it’s a solved problem, that particular problem is solved. And there is an example of the kind of thing that you see. That’s on a piece of 8 by 12 paper. That takes about two seconds to make. And so I regard that as done. There is a very important issue here, which is that because it’s a printer, a color printer, it prints colors. That’s what color printers do. I’ll show you in a moment, that’s actually quite useful.


Now, the next question that you would like to ask is: What would you like to measure? What would you like to analyze? And the thing which you’d most like to analyze, we’re a fair distance from. It’s what’s called “fever of undiagnosed origin.” Someone comes into the clinic, they have a fever, they feel bad. What do they have? Do they have T.B.? Do they have AIDS? Do they have a common cold? The triage problem. That’s a hard problem for reasons that I won’t go through. There are an awful lot of things that you’d like to distinguish among. But then there are a series of things: AIDS, hepatitis, malaria, TB, others and simpler ones, such as guidance of treatment.


Now even that’s more complicated than you think. A friend of mine works in transcultural psychiatry, and he is interested in the question of why people do and don’t take their meds. So, Dapsone, or something like that, you have to take it for a while. He has a wonderful story of talking to a villager in India and saying, “Have you taken your Dapsone?” “Yes.” “Have you taken it every day?” “Yes.” “Have you taken if for a month?” “Yes.” What the guy actually meant was that he’d fed a 30-day dose of Dapsone to his dog, that morning. (Laughter) He was telling the truth. Because in a different culture, the dog is a surrogate for you, you know, “today,” “this month,” “since the rainy season” — there are lots of opportunities for misunderstanding, and so an issue here is to, in some cases, to figure out how to deal with matters that seem uninteresting, like compliance.


Now, take a look at what a typical test looks like. Prick a finger, you get some blood, about 50 microliters. That’s about all you’re going to get, because you can’t use the usual sort of systems. You can’t manipulate it very well, although I’ll show something about that in a moment. So, you take the drop of blood, no further manipulations, you put it on a little device, the device filters out the blood cells, lets the serum go through, and you get a series of colors down in the bottom there. And the colors indicate “disease” or “normal.” But even that’s complicated, because to you, to me, colors might indicate “normal,” but, after all, we’re all suffering from probably an excess of education.


What you do about something which requires quantitative analysis? And so the solution that we and many other people are thinking about there, and at this point there is a dramatic flourish, and out comes the universal solution to everything these days, which is a cell phone. In this particular case, a camera phone. They’re everywhere, six billion a month in India. And the idea is that what one does, is to take the device, you dip it, you develop the color, you take a picture, the picture goes to a central laboratory. You don’t have to send out a doctor, you send out somebody who can just take the sample, and in the clinic either a doctor, or ideally a computer in this case, does the analysis. Turns out to work actually quite well, particularly when your color printer has printed the color bars that indicate how things work.


So, my view of the health care worker of the future is not a doctor, but is an 18-year-old, otherwise unemployed, who has two things: He has a backpack full of these tests, and a lancet to occasionally take a blood sample, and an AK-47. And these are the things that get him through his day.


There’s another very interesting connection here, and that is that what one wants to do is to pass through useful information over what is generally a pretty awful telephone system. It turns out there’s an enormous amount of information already available on that subject, which is the Mars rover problem. How do you get back an accurate view of the color on Mars if you have a really terrible bandwidth to do it with? And the answer is not complicated but it’s one which I don’t want to go through here, other than to say that the communication systems for doing this are really pretty well understood.


Also, a fact which you may not know is that the compute capability of this thing is not so different from the compute capability of your desktop computer. This is a fantastic device which is only beginning to be tapped. I don’t know whether the idea of one computer, one child makes any sense. Here’s the computer of the future, because this screen is already there and they’re ubiquitous.


All right now let me show you just a little bit about advanced devices. And we’ll start by posing a little problem. What you see here is another centimeter-sized device, and the different colors are different colors of dye. And you notice something which might strike you as a little bit interesting, which is the yellow seems to disappear, get through the blue, and then get through the red. How does that happen? How do you make something flow through something? And, of course the answer is, “You don’t.” You make it flow under and over.


But now the question is: How do you make it flow under and over in a piece of paper? The answer is that what you do, and the details are not terribly important here, is to make something more elaborate: You take several different layers of paper, each one containing its own little fluid system, and you separate them by pieces of, literally, double-sided carpet tape, the stuff you use to stick the carpets onto the floor. And the fluid will flow from one layer into the next. It distributes itself, flows through further holes, distributes itself.


And what you see, at the lower right-hand side there, is a sample in which a single sample of blood has been put on the top, and it has gone through and distributed itself into these 16 holes on the bottom, in a piece of paper — basically it looks like a chip, two pieces of paper thick. And in this particular case we were just interested in the replicability of that. But that is, in principle, the way you solve the “fever of unexplained origin” problem, because each one of those spots then becomes a test for a particular set of markers of disease, and this will work in due course.


A lab the size of a postage stamp


Here is an example of a slightly more complicated device. There’s the chip. You dip in a corner. The fluid goes into the center. It distributes itself out into these various wells or holes, and turns color, and all done with paper and carpet tape. So, I think it’s as low-cost as we’re likely to be able to come up and make things.


Now, I have one last, two last little stories to tell you, in finishing off this business. This is one: One of the things that one does occasionally need to do is to separate blood cells from serum. And the question was, here we do it by taking a sample, we put it in a centrifuge, we spin it, and you get blood cells out. Terrific. What happens if you don’t have an electricity, and a centrifuge, and whatever? And we thought for a while of how you might do this and the way, in fact, you do it is what’s shown here. You get an eggbeater, which is everywhere, and you saw off a blade, and then you take tubing, and you stick it on that. You put the blood in, you spin it — somebody sits there and spins it. It works really, really well.


And we sat down, we did the physics of eggbeaters and self-aligning tubes and all the rest of that kind of thing, sent it off to a journal. We were very proud of this, particularly the title, which was “Eggbeater as Centrifuge.” (Laughter) And we sent it off, and by return mail it came back. I called up the editor and I said, “What’s going on? How is this possible?” The editor said, with enormous disdain, “I read this. And we’re not going to publish it, because we only publish science.” And it’s an important issue because it means that we have to, as a society, think about what we value. And if it’s just papers and phys. rev. letters, we’ve got a problem.


Here is another example of something which is — this is a little spectrophotometer. It measures the absorption of light in a sample The neat thing about this is, you have light source that flickers on and off at about 1,000 hertz, another light source that detects that light at 1,000 hertz, and so you can run this system in broad daylight. It performs about equivalently to a system that’s in the order of 100,000 dollars. It costs 50 dollars. We can probably make it for 50 cents, if we put our mind to it. Why doesn’t somebody do it? And the answer is, “How do you make a profit in a capitalist system, doing that?” Interesting problem.


So, let me finish by saying that we’ve thought about this as a kind of engineering problem. And we’ve asked: What is the scientific unifying idea here? And we’ve decided that we should think about this not so much in terms of cost, but in terms of simplicity. Simplicity is a neat word. And you’ve got to think about what simplicity means. I know what it is but I don’t actually know what it means.


So, I actually was interested enough in this to put together several groups of people. And the most recent involved a couple of people at MIT, one of them being an exceptionally bright kid who is one of the very few people I would think of who’s an authentic genius. We all struggled for an entire day to think about simplicity. And I want to give you the answer of this deep scientific thought. (Laughter) So, in a sense, you get what you pay for. Thank you very much. (Laughter)


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The above video is based on materials provided by TED.


19 Kasım 2014 Çarşamba

Scientists prevent memory problems caused by sleep deprivation

from

BIOENGINEER.ORG http://bioengineer.org/scientists-prevent-memory-problems-caused-by-sleep-deprivation/



Sleep is a critical period for memory consolidation, and most people don’t get enough. Research has shown that even brief periods of sleep deprivation can lead to deficits in memory formation. In a new study, published in the Journal of Neuroscience, a team led by scientists from the University of Pennsylvania found that a particular set of cells in a small region of the brain are responsible for memory problems after sleep loss. By selectively increasing levels of a signaling molecule in these cells, the researchers prevented mice from having memory deficits.


Scientists prevent memory problems caused by sleep deprivation



The hippocampus of a mouse in the study glows green, showing where excitatory neurons took up a cAMP-triggering receptor. Photo Credit: Image courtesy of University of Pennsylvania



Robbert Havekes was the lead author on the study. He is a research associate in the lab of Ted Abel, the study’s senior author and Brush Family Professor of Biology in Penn’s School of Arts & Sciences. Coauthors from the Abel lab included Jennifer C. Tudor and Sarah L. Ferri. They collaborated with Arnd Baumann of Forschungszentrum Jülich, Germany, and Vibeke M. Bruinenberg and Peter Meerlo of the University of Groningen, The Netherlands.


In 2009, a group from Abel’s lab published a study in Nature that identified the cyclic AMP, or cAMP, signaling pathway as playing a role in sleep-loss-associated memory problems. Whereas depriving mice of sleep impaired their spatial memory, restoring levels of cAMP in their brain prevented this effect.


“The challenge following this important study,” Abel said, “was to determine if the impact of sleep deprivation was mediated by particular regions of the brain and particular neural circuits. We suspected that the hippocampus, the brain region that mediates spatial navigation and contextual memory, was critical.”


In the current work, they set out to answer these questions. They targeted excitatory neurons because of their importance in transmitting signals in the brain and the fact that their functioning relies on cAMP signaling. The limitation of previous studies was that they lacked a way to increase cAMP in just one area of the brain in a cell-type specific fashion. Havekes, Abel and colleagues devised a way of doing this that they term a “pharmacogenetic” approach, blending genetic modification and drug administration.


They engineered a non-pathogenic virus to harbor the gene encoding the receptor for the protein octopamine, which triggers cAMP pathway activation in fruit flies but is not naturally found in the brains of mice. The researchers injected this virus into the hippocampus of mice so that the excitatory neurons in that region alone would express the octopamine receptor.


“It sounds weird. Why would you put a receptor there that is never going to be activated?” Havekes said. “The trick is, you follow that up by giving mice the ligand of the receptor, which is octopamine, and that will activate the receptors only where they are present.”


The team confirmed that only the excitatory hippocampal neurons expressed the receptor and that they could selectively increase cAMP levels in only these cells by giving the mice a systemic injection of octopamine.


“This way, we could manipulate the cAMP pathways that we previously saw being affected by sleep deprivation but selectively in specific neural circuits in the brain,” Havekes says.


With this pharmacogenetic tool in hand, Havekes, Abel and colleagues began the sleep deprivation tests with the mice expressing the octopamine receptor in their hippocampus. First the researchers trained mice in a spatial memory task. They put them in a box that had three different objects, each in a distinct location.


Then, because previous research had shown that cAMP signaling contributes to hippocampus-dependent memory consolidation in two time windows — first directly after training and again three to four hours after training — the researchers gave mice in the experimental groups injections of octopamine in both of these windows to boost cAMP levels.


Mice receiving the cAMP boost were divided into two groups: One was left to sleep undisturbed, while the other was sleep-deprived for five hours by gently tapping their cage or rearranging their bedding.


One full day after the initial training, all of the mice were tested again. This time, there was a twist: one of the objects originally in the box had been moved to a new location.


“If the mice had learned and remembered the location of the objects during their training, then they would realize, okay, this is the object that has moved, and they’ll spend more time exploring that particular object,” Havekes explained. “If they didn’t remember well, they would explore all the objects in a random fashion.”


The researchers found that the sleep-deprived mice that received the octopamine injections spent more time exploring the object that had moved, just as mice that had not been sleep deprived did. On the other hand, sleep-deprived mice that didn’t express the receptor explored all the objects at random, a sign that they had failed to remember the locations of the objects from their initial training as a result of the brief period of sleep deprivation.


“What we’ve shown is this memory loss due to sleep deprivation is really dependent on misregulation of cAMP signaling in the excitatory neurons of the hippocampus,” Havekes said.


As a next step, the group would like to explore what cAMP is doing to help consolidate memory. They would also like to investigate how other cell types in the brain, such as astrocytes, might be affected. And finally, while this study focused on the impact of a brief period of sleep deprivation, Havekes is curious to know how not getting enough sleep on a daily basis, as is more similar to human experiences, might be affecting memory.


“Thinking about people who do shift work or doctors who work long hours, if we can tackle the cognitive problems that result from sleep loss, that would be a great thing,” Havekes said.


“At least in the mouse using these sophisticated tools, we’re able to reverse the negative impact of sleep deprivation on cognition,” Abel said.


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The above story is based on materials provided by University of Pennsylvania.


Training can lead to synaesthetic experiences

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BIOENGINEER.ORG http://bioengineer.org/training-can-lead-to-synaesthetic-experiences/



A new study has shown for the first time that people can be trained to “see” letters of the alphabet as colours in a way that simulates how those with synaesthesia experience their world.


Training can lead to synaesthetic experiences



Photo Credit: University of Sussex



The University of Sussex research, published today (18 November 2014) in Scientific Reports, also found that the training might potentially boost IQ.


Synaesthesia is a fascinating though little-understood neurological condition in which some people (estimated at around 1 in 23) experience an overlap in their senses. They “see” letters as specific colours, or can “taste” words, or associate sounds with different colours.


A critical debate concerns whether the condition is embedded in our genes, or whether it emerges because of particular environmental influences, such as coloured-letter toys in infancy.


While the two possibilities are not mutually exclusive, psychologists at the University’s Sackler Centre for Consciousness Science devised a nine-week training programme to see if adults without synaesthesia can develop the key hallmarks of the condition.


They found, in a sample study of 14, that not only were the participants able to develop strong letter-colour associations to pass all the standard tests for synaesthesia, most also experienced sensations such as letters seeming “coloured” or having individual personas (for instance, “x is boring”, “w is calm”).


One of the most surprising outcomes of the study was that those who underwent the training also saw their IQ jump by an average of 12 points, compared to a control group that didn’t undergo training.


Dr Daniel Bor, who co-led the study with Dr Nicolas Rothen, says: “The main implication of our study is that radically new ways of experiencing the world can be brought about simply through extensive perceptual training.


“The cognitive boost, although provisional, may eventually lead to clinical cognitive training tools to support mental function in vulnerable groups, such as Attention Deficit Hyperactivity (ADHD) children, or adults starting to suffer from dementia.”


Dr Rothen adds: “It should be emphasised that we are not claiming to have trained non-synaesthetes to become genuine synaesthetes. When we retested our participants three months after training, they had largely lost the experience of ‘seeing’ colours when thinking about the letters. But it does show that synaesthesia is likely to have a major developmental component, starting for many people in childhood.”


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The above story is based on materials provided by University of Sussex.


Hacking health care

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BIOENGINEER.ORG http://bioengineer.org/hacking-health-care/



PhD student Andrea Ippolito improves health care through engineering, entrepreneurship, and systems design.For as long as she can remember, Andrea Ippolito has known that she wanted to be an engineer.

What she couldn’t have predicted was what, precisely, the scope and scale of her work would turn out to be.


Hacking health care



Andrea Ippolito Photo Credit: Allegra Boverman



Ippolito began her career at Boston Scientific after getting bachelor’s and master’s degrees in biomedical engineering from Cornell University. Back then, she worked on drug-coated medical devices and studied how they interfaced with the surrounding cells of a patient.


She liked working on those systems, but also began fostering an interest in health care engineering on a more macroscopic scale: Rather than one device, one human, or one interface, Ippolito wanted to look at the entire health care ecosystem.


“I was drawn into the strategy of the technology as well as the technology,” she says.

It was that newfound fascination that brought her to the MIT System Design and Management (SDM) program in 2011, and then to the Engineering Systems Division (ESD) PhD program in 2013. Today, Ippolito is a second-year graduate student in ESD, expecting to earn her PhD in 2017.


Ippolito’s initial research focused on the use of “telehealth” — treatment via video chat — and in particular on the treatment of post-traumatic stress disorder (PTSD) within military health systems. The problem is that when members of the military return from deployment, they often do so in large numbers. As a result, the health care providers that administer PTSD screenings are overwhelmed with work.


Telehealth treatment could make it easier to spread out workloads for overall better care and more predictable scheduling. It could also enable the standardization of certain health care best practices, a boon for a complex health care network like that of the U.S. military.


Presidential honor


Earlier this fall, Ippolito was named by the White House and General Services Administration as a Presidential Innovation Fellow, allowing her to work directly with the Department of Veterans Affairs to improve some of its processes.


“The Presidential Innovation Fellowship program is a wonderful opportunity to reimagine new ways of approaching complex, system-level challenges facing our country through the stage of the federal government,” Ippolito told the website Medtech Boston last month. “I am thrilled to be working with the Department of Veterans Affairs to help serve our nation’s veterans, who have sacrificed so much for our country.”


“As a member of the team at the VA Center for Innovation,” she added, “I am excited to work on the design, planning, and initial execution for a VA Innovator’s Network intended to resolve the challenges restricting in-depth collaboration across the [VA].”


As her research progresses, Ippolito continues to focus on how technology can enable a better, cheaper, and more navigable health care system. Last fall, she worked on a project evaluating the Massachusetts Health Information Exchange, the network by which patient records are shared among health care providers and other members of the health care ecosystem.


“I got a great bird’s-eye view of all the different entities and got to really understand the complexity of our health care system,” she says.


“There’s such an imperative right now to contain costs and improve access,” she adds. “I’m interested in how to accelerate that trajectory.”


Deep roots in engineering


Ippolito has admired the practices of scientists and engineers since she was a young girl. It’s in her blood: Her father was a mechanical engineer, and her mother was an electrical engineer who designed space suits.


During recess while in grade school, Ippolito would play on the playground like the other kids — but her favorite spot was a big rock in the schoolyard, which she would pretend was her own personal laboratory. In sixth grade, she dressed up as astronaut Sally Ride for Halloween — no doubt inspired, in part, by her mother’s work — and did most years after that.


“I was really lucky I had such a positive role model in my mom,” Ippolito says.


Ippolito always wanted to go to space camp, too, but her mother said it was too expensive — “which it sort of is, for a little kid for five days,” she concedes. So after she graduated from MIT SDM, she and her mother celebrated by finally going to space camp.


Ippolito might not have ended up in the field of health care were it not for several biology teachers and mentors she encountered during high school in Burlington, Mass. In particular, she recalls attending a national leadership forum on medicine one summer in Philadelphia. At the forum, she met a biomedical engineer from Shriners Hospital for Children who ran a “gait lab” — attaching sensors to kids with motor disabilities to study and try to improve their gaits. Ippolito was fascinated, and asked the engineer about his work.


That was the first time she heard the term “biomedical engineering”; several years later, she had a degree in the discipline from Cornell.


Pursuing innovation on all fronts


Ippolito is working on improving health care systems through entrepreneurship as well as her research.

She’s a co-lead of the MIT student organization Hacking Medicine, whose goal is to apply agile, disruptive thinking to big problems in the health care sphere. So far, Hacking Medicine has held nearly 20 hackathons in the United States, Spain, Uganda, and India.


Often, these health care hack days spark new startups. One of Ippolito’s favorites is PillPack, an online pharmacy that provides medications pre-sorted into packs grouped by when the medication should be taken. PillPack has raised nearly $13 million in funding.


Ippolito’s own startup, Smart Scheduling, also resulted from a Hacking Medicine event. Smart Scheduling was born from the realization that patient no-shows are a giant inefficiency, and a burden on doctors. Doctors fight no-shows by overbooking patients, which is not ideal because if patients do show up, there’s not enough room to fit them in the schedule. Smart Scheduling uses machine learning to identify potential no-shows to take better care of patients by providing better appointment access and schedule flexibility.


Overall, Ippolito is applying every tool in her toolkit — entrepreneurship, system design, and engineering expertise — to her obsession with improving the health care ecosystem.

“I just think that being an engineer in health care, there’s no better place to be to make an impact,” she says.


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The above story is based on materials provided by MIT News Office.


Two sensors in one

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BIOENGINEER.ORG http://bioengineer.org/two-sensors-in-one/



MIT chemists have developed new nanoparticles that can simultaneously perform magnetic resonance imaging (MRI) and fluorescent imaging in living animals. Such particles could help scientists to track specific molecules produced in the body, monitor a tumor’s environment, or determine whether drugs have successfully reached their targets.


Two sensors in one



Photo Illustration: Christine Daniloff/MIT



In a paper appearing in the Nov. 18 issue of Nature Communications, the researchers demonstrate the use of the particles, which carry distinct sensors for fluorescence and MRI, to track vitamin C in mice. Wherever there is a high concentration of vitamin C, the particles show a strong fluorescent signal but little MRI contrast. If there is not much vitamin C, a stronger MRI signal is visible but fluorescence is very weak.


Future versions of the particles could be designed to detect reactive oxygen species that often correlate with disease, says Jeremiah Johnson, an assistant professor of chemistry at MIT and senior author of the study. They could also be tailored to detect more than one molecule at a time.

“You may be able to learn more about how diseases progress if you have imaging probes that can sense specific biomolecules,” Johnson says.


Dual action


Johnson and his colleagues designed the particles so they can be assembled from building blocks made of polymer chains carrying either an organic MRI contrast agent called a nitroxide or a fluorescent molecule called Cy5.5.


When mixed together in a desired ratio, these building blocks join to form a specific nanosized structure the authors call a branched bottlebrush polymer. For this study, they created particles in which 99 percent of the chains carry nitroxides, and 1 percent carry Cy5.5.


Nitroxides are reactive molecules that contain a nitrogen atom bound to an oxygen atom with an unpaired electron. Nitroxides suppress Cy5.5’s fluorescence, but when the nitroxides encounter a molecule such as vitamin C from which they can grab electrons, they become inactive and Cy5.5 fluoresces.


Nitroxides typically have a very short half-life in living systems, but University of Nebraska chemistry professor Andrzej Rajca, who is also an author of the new Nature Communications paper, recently discovered that their half-life can be extended by attaching two bulky structures to them. Furthermore, the authors of the Nature Communications paper show that incorporation of Rajca’s nitroxide in Johnson’s branched bottlebrush polymer architectures leads to even greater improvements in the nitroxide lifetime. With these modifications, nitroxides can circulate for several hours in a mouse’s bloodstream — long enough to obtain useful MRI images.


The researchers found that their imaging particles accumulated in the liver, as nanoparticles usually do. The mouse liver produces vitamin C, so once the particles reached the liver, they grabbed electrons from vitamin C, turning off the MRI signal and boosting fluorescence. They also found no MRI signal but a small amount of fluorescence in the brain, which is a destination for much of the vitamin C produced in the liver. In contrast, in the blood and kidneys, where the concentration of vitamin C is low, the MRI contrast was maximal.


Mixing and matching


The researchers are now working to enhance the signal differences that they get when the sensor encounters a target molecule such as vitamin C. They have also created nanoparticles carrying the fluorescent agent plus up to three different drugs. This allows them to track whether the nanoparticles are delivered to their targeted locations.


“That’s the advantage of our platform — we can mix and match and add almost anything we want,” Johnson says.


These particles could also be used to evaluate the level of oxygen radicals in a patient’s tumor, which can reveal valuable information about how aggressive the tumor is.

“We think we may be able to reveal information about the tumor environment with these kinds of probes, if we can get them there,” Johnson says. “Someday you might be able to inject this in a patient and obtain real-time biochemical information about disease sites and also healthy tissues, which is not always straightforward.”


Steven Bottle, a professor of nanotechnology and molecular science at Queensland University of Technology, says the most impressive element of the study is the combination of two powerful imaging techniques into one nanomaterial.


“I believe this should deliver a very powerful, metabolically linked, multi-combination imaging modality which should provide a highly useful diagnostic tool with real potential to follow disease progression in vivo,” says Bottle, who was not involved in the study.


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The above story is based on materials provided by MIT News Office.