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Phytophthora root rot in the NY Times: Building a Better Christmas Tree (2012)

Phytophthora root rot in the NY Times: Building a Better Christmas Tree (2012) | WWWBiology | Scoop.it

Researchers are trying to develop a Christmas tree that will hold onto its needles from Thanksgiving to New Year’s — not a small thing in a $1 billion industry.

 

From Lab to Living Room - A typical tree can take from 8 to 12 years to go from seed cone to Christmas tree stand.

 

The largest Christmas tree operations harvest almost a million trees a year, transporting them by helicopter.

 

A small operation like Bell’s Christmas Tree Farm might raise fewer than 30,000 trees.

 

Before a seedling arrives at a small farm, it may have been germinated by a large forestry company and transplanted several times at a third nursery.

 

The quest for a better tree has led growers to look beyond favorites like blue spruce (below) to less common varieties, like Turkish, Korean and Canaan firs.

 

Organic Christmas tree farms are rare. Growers typically use pesticides to control blights like Phytophthora root rot and Swiss needle cast.


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Two huge magma chambers sit beneath Yellowstone National Park

Two huge magma chambers sit beneath Yellowstone National Park | WWWBiology | Scoop.it
Underneath the bubbling geysers and hot springs of Yellowstone National Park in Wyoming sits a volcanic hot spot that has driven some of the largest eruptions on Earth. Geoscientists have now completely imaged the subterranean plumbing system and have found not just one, but two magma chambers underneath the giant volcano.

“The main new thing is we unveil a deeper and bigger magma reservoir in the lower crust,” says study author Hsin-Hua Huang, a seismologist at the University of Utah in Salt Lake City.

Scientists had already known about a plume, which brings molten rock up from deep in the mantle to a region about 60 kilometers below the surface. And they had also imaged a shallow magma chamber about 10 kilometers below the surface, containing about 10,000 cubic kilometers of molten material. But now they have found a deeper one, 4.5 times larger, that sits between 20 and 50 kilometers below the surface. “They found the missing link between the mantle plume and the shallow magma chamber,” says Peter Cervelli, a geophysicist in Anchorage, Alaska, who works at the U.S. Geological Survey’s Yellowstone Volcano Observatory.

The discovery does not, on its own, increase the chance of an eruption, which is driven by an emptying of the shallow chamber. The last major eruption was 640,000 years ago, and today the threat of earthquakes is far more likely. But the deeper chamber does mean that the shallow chamber can be replenished again and again. “Knowing that you have this additional reservoir tells you you could have a much bigger volume erupt over a relatively short time scale,” says co-author Victor Tsai, a geophysicist at the California Institute of Technology in Pasadena. The discovery, reported online today in Science, also confirms a long-suspected model for some volcanoes, in which a deep chamber of melted basalt, a dense iron- and magnesium-rich rock, feeds a shallower chamber containing a melted, lighter silicon-rich rock called a rhyolite.

The researchers used seismometers to measure the noise of earthquakes in order to take a sort of sonogram of Earth’s crust. When earthquakes pass through liquid material, seismic waves slow down. The team interprets these low-velocity regions as magma chambers (although these chambers are still mostly solid rock and contain only a small fraction of liquid melt). Distant earthquakes are useful for imaging deep structures, like the mantle plume, and local earthquakes can help to see the shallow chamber. Huang says his study is the first time that both types of data were combined so that the middle depths, and the deeper chamber, could be seen. His team used 11 seismometers from the EarthScope USArray to listen for the deep earthquakes and 69 seismometers from several local seismic networks to gather data from shallower earthquakes.

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New insight into how brain makes memories

New insight into how brain makes memories | WWWBiology | Scoop.it

Every time you make a memory, somewhere in your brain a tiny filament reaches out from one neuron and forms an electrochemical connection to a neighboring neuron. A team of biologists at Vanderbilt University, headed by Associate Professor of Biological Sciences Donna Webb, studies how these connections are formed at the molecular and cellular level.


The filaments that make these new connections are called dendritic spines and, in a series of experiments described in the April 17 issue of the Journal of Biological Chemistry, the researchers report that a specific signaling protein, Asef2, a member of a family of proteins that regulate cell migration and adhesion, plays a critical role in spine formation. This is significant because Asef2 has been linked to autism and the co-occurrence of alcohol dependency and depression.


"Alterations in dendritic spines are associated with many neurological and developmental disorders, such as autism, Alzheimer's disease and Down Syndrome," said Webb. "However, the formation and maintenance of spines is a very complex process that we are just beginning to understand."


Neuron cell bodies produce two kinds of long fibers that weave through the brain: dendrites and axons. Axons transmit electrochemical signals from the cell body of one neuron to the dendrites of another neuron. Dendrites receive the incoming signals and carry them to the cell body. This is the way that neurons communicate with each other.


As they wait for incoming signals, dendrites continually produce tiny flexible filaments called filopodia. These poke out from the surface of the dendrite and wave about in the region between the cells searching for axons. At the same time, biologists think that the axons secrete chemicals of an unknown nature that attract the filopodia. When one of the dendritic filaments makes contact with one of the axons, it begins to adhere and to develop into a spine. The axon and spine form the two halves of a synaptic junction. New connections like this form the basis for memory formation and storage.


The formation of spines is driven by actin, a protein that produces microfilaments and is part of the cytoskeleton. Webb and her colleagues showed that Asef2 promotes spine and synapse formation by activating another protein called Rac, which is known to regulate actin activity. They also discovered that yet another protein, spinophilin, recruits Asef2 and guides it to specific spines. "Once we figure out the mechanisms involved, then we may be able to find drugs that can restore spine formation in people who have lost it, which could give them back their ability to remember," said Webb.


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DNA 'cage' holding a payload of drugs set to begin clinical trial soon

DNA 'cage' holding a payload of drugs set to begin clinical trial soon | WWWBiology | Scoop.it

Ido Bachelet, who was previously at Harvard’s Wyss Institute in Boston, Massachusetts and Israel’s Bar-Ilan University, intends to treat a patient who has been given six months to live. The patient is set to receive an injection of DNA nanocages designed to interact with and destroy leukemia cells without damaging healthy tissue. Speaking in December, he said: ‘Judging from what we saw in our tests, within a month that person is going to recover.


DNA nanocages can be programmed to independently recognize target cells and deliver payloads, such as cancer drugs, to these cells. 

George Church, who is involved in the research at the Wyss Institute explained the idea of the microscopic robots is to make a ‘cage’ that protects a fragile or toxic payload and ‘only releases it at the right moment.’


These nanostructures are built upon a single strand of DNA which is combined with short synthetic strands of DNA designed by the experts.  When mixed together, they self-assemble into a desired shape, which in this case looks a little like a barrel.


Dr Bachelet said: 'The nanorobot we designed actually looks like an open-ended barrel, or clamshell that has two halves linked together by flexible DNA hinges and the entire structure is held shut by latches that are DNA double helixes.’


A complementary piece of DNA is attached to a payload, which enables it to bind to the inside of the biological barrel. The double helixes stay closed until specific molecules or proteins on the surface of cancer cells act as a 'key' to open the ‘barrel’ so the payload can be deployed.


'The nanorobot is capable of recognizing a small population of target cells within a large healthy population,’ Dr Bachelet continued.

‘While all cells share the same drug target that we want to attack, only those target cells that express the proper set of keys open the nanorobot and therefore only they will be attacked by the nanorobot and by the drug.’


The team has tested its technique in animals as well as cell cultures and said the ‘nanorobot attacked these [targets] with almost zero collateral damage.’ The method has many advantages over invasive surgery and blasts of drugs, which can be ‘as painful and damaging to the body as the disease itself,’ the team added.


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Man builds low-cost tiny home with recycled materials for $500

Man builds low-cost tiny home with recycled materials for $500 | WWWBiology | Scoop.it
Compact but filled with light, storage and clever ideas, this tiny house's budget was kept low by using salvaged or gifted materials.

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New species of leprosy bacteria found

New species of leprosy bacteria found | WWWBiology | Scoop.it

Scientists have compared for the first time the genomes of the two bacteria species that cause leprosy. The study shows how the two species evolved from a common ancestor around 13.9 million years ago, and offers new insights into their biology that could lead to new treatments.


Leprosy is a chronic infection of the skin, peripheral nerves, eyes and mucosa of the upper respiratory tract, affecting over a quarter million people worldwide. Its symptoms can be gruesome and devastating, as the bacteria reduce sensitivity in the body, resulting in skin lesions, nerve damage and disabilities. Until recently, leprosy was attributed to a single bacterium, Mycobacterium leprae; we now suspect that its close relative, Mycobacterium lepromatosis, might cause a rare but severe form of leprosy. EPFL scientists have analyzed for the first time the complete genome of M. lepromatosis, and compared it to that of the major leprosy-causing bacterium.


Published in PNAS, the study reveals the origin and evolutionary history of both bacteria, and offers new insights into their biology, global distribution, and possibly treatment. Along with its mutilating symptoms, leprosy also carries a stigma, turning patients into social outcasts. Although we have been able to push back the disease with antibiotics, leprosy remains endemic in many developing countries today.


Leprosy can manifest itself in various forms, all thought to be caused by the bacterium M. leprae. But in 2008, a study showed considerable evidence that another species of bacterium, M. lepromatosis, causes a distinct and aggressive form of the disease called “diffuse lepromatous leprosy”, found in Mexico and the Caribbean.


The lab of Stewart Cole at EPFL’s Global Health Institute carried out a genome-wide investigation on M. lepromatosis. This complex and computer-heavy technique looks at the bacterium’s entire DNA, locating its genes along the sequence. Because M. lepromatosis cannot be grown in the lab and animal models for this version of leprosy do not exist yet, the scientists used an infected skin sample from a patient in Mexico to obtain the bacterium’s genetic material.


After extracting the DNA from the entire sample, the researchers had to separate the bacterial DNA from the patient’s. To do this, they used two genetic techniques: one that increased the bacterium’s DNA and another that decreased the human DNA. With the bacterium’s DNA isolated, the researchers were able to sequence it and read it. Once they had the complete sequence of the bacterium’s genome, they were able to compare it with the known genome of M. leprae, the bacterium responsible for the majority of leprosy cases.


The study found that the two species of bacteria are very closely related. The comparative genomics analysis could “backtrack” the history of their genes, and showed that the two bacteria have diverged 13.9 million years ago from a common ancestor with a similar genome structure, and possibly a similar lifestyle. That ancestor suffered a process known as “gene decay”, where over a long period of time and multiple generations, a large number of genes mutated, became non-functional, and eventually disappeared. The study showed that the two new species continued to lose genes but from different regions of their genomes, indicating that during their evolution they occupied different biological roles and mechanisms to ensure survival.



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Long-standing mystery in membrane traffic finally solved

Long-standing mystery in membrane traffic finally solved | WWWBiology | Scoop.it

SNARE proteins are known as the minimal machinery for membrane fusion. To induce membrane fusion, the proteins combine to form a SNARE complex in a four helical bundle, and NSF and α-SNAP disassemble the SNARE complex for reuse. In particular, NSF can bind an energy source molecule, adenosine triphosphate (ATP), and the ATP-bound NSF develops internal tension via cleavage of ATP. This process is used to exert great force on SNARE complexes, eventually pulling them apart. However, although about 30 years have passed since the Nobel Prize winners' discovery, how NSF/α-SNAP disassembled the SNARE complex remained a mystery to scientists due to a lack in methodology.


In a recent issue of Science, published on March 27, 2015, a research team, led by Tae-Young Yoon of the Department of Physics at the Korea Advanced Institute of Science and Technology (KAIST) and Reinhard Jahn of the Department of Neurobiology of the Max-Planck-Institute for Biophysical Chemistry, reports that NSF/α-SNAP disassemble a single SNARE complex using various single-molecule biophysical methods that allow them to monitor and manipulate individual protein complexes. "We have learned that NSF releases energy in a burst within 20 milliseconds to "tear" the SNARE complex apart in a one-step global unfolding reaction, which is immediately followed by the release of SNARE proteins," said Yoon.


Previously, it was believed that NSF disassembled a SNARE complex by unwinding it in a processive manner. Also, largely unexplained was how many cycles of ATP hydrolysis were required and how these cycles were connected to the disassembly of the SNARE complex.


Yoon added, "From our research, we found that NSF requires hydrolysis of ATPs that were already bound before it attached to the SNAREs--which means that only one round of an ATP turnover is sufficient for SNARE complex disassembly. Moreover, this is possible because NSF pulls a SNARE complex apart by building up the energy from individual ATPs and releasing it at once, yielding a "spring-loaded" mechanism."


NSF is a member of the ATPases associated with various cellular activities family (AAA+ ATPase), which is essential for many cellular functions such as DNA replication and protein degradation, membrane fusion, microtubule severing, peroxisome biogenesis, signal transduction, and the regulation of gene expression. This research has added valuable new insights and hints for studying AAA+ ATPase proteins, which are crucial for various living beings.

 

Reference: "Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover." (DOI: 10.1126/science.aaa5267)

 

Youtube Link: https://www.youtube.com/watch?v=FqTSYHtyHWE&feature=youtu.be


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Risto Suoknuuti's curator insight, March 29, 6:28 PM

Back to the roots.

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'Google Maps' for the body: A biomedical revolution down to a single cell

'Google Maps' for the body: A biomedical revolution down to a single cell | WWWBiology | Scoop.it
Scientists are using previously top-secret technology to zoom through the human body down to the level of a single cell. Scientists are also using cutting-edge microtome and MRI technology to examine how movement and weight bearing affects the movement of molecules within joints, exploring the relationship between blood, bone, lymphatics and muscle.

 

UNSW biomedical engineer Melissa Knothe Tate is using previously top-secret semiconductor technology to zoom through organs of the human body, down to the level of a single cell.


A world-first UNSW collaboration that uses previously top-secret technology to zoom through the human body down to the level of a single cell could be a game-changer for medicine, an international research conference in the United States has been told.


The imaging technology, developed by high-tech German optical and industrial measurement manufacturer Zeiss, was originally developed to scan silicon wafers for defects.


UNSW Professor Melissa Knothe Tate, the Paul Trainor Chair of Biomedical Engineering, is leading the project, which is using semiconductor technology to explore osteoporosis and osteoarthritis.


Using Google algorithms, Professor Knothe Tate -- an engineer and expert in cell biology and regenerative medicine -- is able to zoom in and out from the scale of the whole joint down to the cellular level "just as you would with Google Maps," reducing to "a matter of weeks analyses that once took 25 years to complete."


Her team is also using cutting-edge microtome and MRI technology to examine how movement and weight bearing affects the movement of molecules within joints, exploring the relationship between blood, bone, lymphatics and muscle. "For the first time we have the ability to go from the whole body down to how the cells are getting their nutrition and how this is all connected," said Professor Knothe Tate. "This could open the door to as yet unknown new therapies and preventions."


Professor Knothe Tate is the first to use the system in humans. She has forged a pioneering partnership with the US-based Cleveland Clinic, Brown and Stanford Universities, as well as Zeiss and Google to help crunch terabytes of data gathered from human hip studies. Similar research is underway at Harvard University and Heidelberg in Germany to map neural pathways and connections in the brains of mice.


The above story is based on materials provided by University of New South Wales.


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CineversityTV's curator insight, March 30, 8:53 PM

What happens with the metadata? In the public domain? Or in the greed hands of the elite.

Courtney Jones's curator insight, April 2, 4:49 AM

,New advances in biomedical technology

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First detailed microscopy images of ultra-small bacteria captured, believed to be as small as life can get

First detailed microscopy images of ultra-small bacteria captured, believed to be as small as life can get | WWWBiology | Scoop.it

The existence of ultra-small bacteria (aka “nanobacteria” or “nannobacteria”) has been debated for two decades, but there hasn’t been a comprehensive electron microscopy and DNA-based description of the microbes until now. They are about 200 nanometers (.2 micrometers) in width with a volume of only about 9 cubic nanometers. About 150 of these bacteria could fit inside an Escherichia coli bacteria cell.


The diverse bacteria were found in groundwater and are thought to be quite common. This is the smallest a cell can be and still accommodate enough material to sustain life, the researchers say. The bacterial cells have densely packed spirals that are probably DNA, a very small number of ribosomes, hair-like appendages, and a stripped-down metabolism that likely requires them to rely on other bacteria for many of life’s necessities.


“These newly described ultra-small bacteria are an example of a subset of the microbial life on earth that we know almost nothing about,” says Jill Banfield, a Senior Faculty Scientist in Berkeley Lab’s Earth Sciences Division and a UC Berkeley professor in the departments of Earth and Planetary Science and Environmental Science, Policy and Management.


“They’re enigmatic. These bacteria are detected in many environments and they probably play important roles in microbial communities and ecosystems. But we don’t yet fully understand what these ultra-small bacteria do,” says Banfield. To concentrate these cells in a sample, they filtered groundwater collected at Rifle, Colorado through successively smaller filters, down to 0.2 microns, which is the size used to sterilize water.


The frozen samples were transported to Berkeley Lab, where Birgit Luef, a former postdoctoral researcher in Banfield’s group characterized the cells’ size and internal structure using 2D and 3D cryogenic transmission electron microscopy. The images revealed dividing cells, indicating the bacteria were healthy and not starved to an abnormally small size.


The bacteria’s genomes were sequenced at the Joint Genome Institute, a DOE Office of Science User Facility located in Walnut Creek, California. The genomes were about one million base pairs in length.


Among their findings: Some of the bacteria have thread-like appendages, called pili, which could serve as “life support” connections to other microbes, and the bacteria lack many basic functions, so they likely rely on a community of microbes for critical resources.



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How blood group O protects against malaria

How blood group O protects against malaria | WWWBiology | Scoop.it
Malaria is a serious disease that is estimated by the WHO to infect 200 million people a year, 600,000 of whom, primarily children under five, fatally. Malaria, which is most endemic in sub-Saharan Africa, is caused by different kinds of parasites from the plasmodium family, and effectively all cases of severe or fatal malaria come from the species known as Plasmodium falciparum. In severe cases of the disease, the infected red blood cells adhere excessively in the microvasculature and block the blood flow, causing oxygen deficiency and tissue damage that can lead to coma, brain damage and, eventually death. Scientists have therefore been keen to learn more about how this species of parasite makes the infected red blood cells so sticky.

It has long been known that people with blood type O are protected against severe malaria, while those with other types, such as A, often fall into a coma and die. Unpacking the mechanisms behind this has been one of the main goals of malaria research.

A team of scientists led from Karolinska Institutet in Sweden have now identified a new and important piece of the puzzle by describing the key part played by the RIFIN protein. Using data from different kinds of experiment on cell cultures and animals, they show how the Plasmodium falciparum parasite secretes RIFIN, and how the protein makes its way to the surface of the blood cell, where it acts like glue. The team also demonstrates how it bonds strongly with the surface of type A blood cells, but only weakly to type O.

Principal investigator Mats Wahlgren, a Professor at Karolinska Institutet's Department of Microbiology, Tumour and Cell Biology, describes the finding as "conceptually simple". However, since RIFIN is found in many different variants, it has taken the research team a lot of time to isolate exactly which variant is responsible for this mechanism.

"Our study ties together previous findings", said Professor Wahlgren. "We can explain the mechanism behind the protection that blood group O provides against severe malaria, which can, in turn, explain why the blood type is so common in the areas where malaria is common. In Nigeria, for instance, more than half of the population belongs to blood group O, which protects against malaria."

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Is whole-genome sequencing for newborns coming?

Is whole-genome sequencing for newborns coming? | WWWBiology | Scoop.it

The advent and refinement of sequencing technologies has resulted in a decrease in both the cost and time needed to generate data on the entire sequence of the human genome. This has increased the accessibility of using whole-genome sequencing and whole-exome sequencing approaches for analysis in both the research and clinical contexts. The expectation is that more services based on these and other high-throughput technologies will become available to patients and the wider population. Some authors predict that sequencing will be performed once in a lifetime, namely, shortly after birth. The Public and Professional Policy Committee of the European Society of Human Genetics, the Human Genome Organization Committee on Ethics, Law and Society, the PHG Foundation and the P3G International Pediatric Platform address herein the important issues and challenges surrounding the potential use of sequencing technologies in publicly funded newborn screening (NBS) programs. This statement presents the relevant issues and culminates in a set of recommendations to help inform and guide scientists and clinicians, as well as policy makers regarding the necessary considerations for the use of genome sequencing technologies and approaches in NBS programs. The primary objective of NBS should be the targeted analysis and identification of gene variants conferring a high risk of preventable or treatable conditions, for which treatment has to start in the newborn period or in early childhood.


The development of next-generation sequencing (NGS) technologies has substantially reduced both the cost and the time required to sequence an entire human genome. The prospect of the availability of NGS technologies and consequently the greater facility to conduct whole-genome sequencing (WGS) have led some to predict that the use of this technology will change the current practice of medicine and public health by enabling more accurate, sophisticated and cost-effective genetic testing.1 It is anticipated that in the short term, the implementation of WGS in the clinic will improve diagnosis and management of some disorders with a strong heritable component,2 as well as improve personalized diagnosis and personalized drug therapy and treatment.


Presently, NGS is being used for targeted sequencing of sets of genes to help guide cancer treatment, and a number of cancer centers are considering using WGS or whole-exome sequencing (WES) in the future. During pregnancy, noninvasive prenatal testing for aneuploidy is also being done using NGS.3 In the clinic, WGS and WES are also being used to identify the causes of rare genetic diseases especially in children4 and in individuals with ‘atypical manifestations, (that) are difficult to confirm using clinical or laboratory criteria alone, or otherwise require extensive or costly evaluation’.5 Disorders for which WGS has been used as a diagnostic tool are usually genetically heterogeneous and have variable phenotypic expression such as intellectual disability, congenital malformations and mitochondrial dysfunctions.5 Other foreseen applications include tissue matching, disease risk predictions, reproductive risk information, forensics or even recreational genomic information (such as genealogy or nonmedically related traits).

 

Nonetheless, Goldenberg and Sharp6 predict that ‘it is likely that the earliest applications of whole-genome sequencing will be restricted to settings in which genetic testing is already a routine part of clinical or public health practice, such as state newborn screening (NBS) programs’.6 In truth, it should be noted that DNA testing, per se, is not a routine part of NBS and that only a very small proportion of babies, depending on the country, have a DNA test (as opposed to a biochemical test).7


Furthermore, the above prediction could be criticized as the routine nature of NBS with its often implied consent, together with its public health context, and the particular vulnerability of the population tested, would make it an unsuitable context into which to first welcome a WGS approach.


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Researchers Produce First Map of New York City Subway System Microbes

Researchers Produce First Map of New York City Subway System Microbes | WWWBiology | Scoop.it

The microbes that call the New York City subway system home are mostly harmless, but include samples of disease-causing bacteria that are resistant to drugs — and even DNA fragments associated with anthrax and Bubonic plague — according to a citywide microbiome map published today by Weill Cornell Medical College investigators.


The study, published in Cell Systems, demonstrates that it is possible and useful to develop a "pathogen map" — dubbed a "PathoMap" — of a city, with the heavily traveled subway a proxy for New York's population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, says the study's senior investigator, Dr. Christopher E. Mason, an assistant professor in Weill Cornell's Department of Physiology and Biophysics and in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine (ICB).

 

The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.


Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists' fingertips.


"Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract," Dr. Mason says. "These bacteria may even be helpful, since they can out-compete any dangerous bacteria."

 

But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.

 

Yet these apparently virulent organisms are not linked to widespread sickness or disease, Dr. Mason says. "They are instead likely just the co-habitants of any shared urban infrastructure and city, but wider testing is needed to confirm this."



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Glassed-in DNA data storage makes the ultimate time capsule, up to 2 million years storage time

Glassed-in DNA data storage makes the ultimate time capsule, up to 2 million years storage time | WWWBiology | Scoop.it

IF YOU must preserve messages for people in the far future to read, Blu-ray discs and USB sticks are no good. For real long-term storage, you want a DNA time capsule. Just 1 gram of DNA is theoretically capable of holding 455 exabytes – enough for all the data held by Google, Facebook and every other major tech company, with room to spare. It's also incredibly durable: DNA has been extracted and sequenced from 700,000-year-old horse bones. But conditions have to be right for it to last.


"We know that if you just store it lying around, you lose information," saysRobert Grass of the Swiss Federal Institute of Technology in Zurich. So he and colleagues are working on ways to increase DNA's longevity, with the aim of storing data for thousands or millions of years.


They began by looking at the way information is encoded on a DNA strand. The simplest method treats the DNA bases A and C as a "0" and G and T as a "1". Of course, any damage to the DNA leaves holes in the data, so the team used an error-correcting technique called a Reed-Solomon code. This includes redundant blocks that can be used to reconstruct garbled bits of data.


They also tried to mimic the way fossils keep a DNA sequence intact. Excluding all water from the environment was key, so they encapsulated the DNA in microscopic spheres of glass.


To test how long this storage system might last, they encoded two venerable documents, totalling 83 kilobytes: the Swiss federal charter from 1291, and the Archimedes Palimpsest, a 10th-century version of ancient Greek texts. DNA versions of these texts were kept at 60, 65 and 70 °C for a week to simulate ageing. They remained readable without any errors (Angewandte Chemie,doi.org/f23gmf).


The results suggest that data in DNA form could last 2000 years if kept at a temperature of around 10 °C. The Global Seed Vault in the Arctic could preserve it for over 2 million years at a chilly -18 °C, offering truly long-term storage.


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Oil Eating Microbes Have Worldwide Underground Connections With Each Other

Oil Eating Microbes Have Worldwide Underground Connections With Each Other | WWWBiology | Scoop.it

Living deep underground ain't easy. In addition to hellish temperatures and pressures, there's not a lot to eat. Which is why oil reservoirs are the microbes’ cornucopia in this hidden realm. 

Microbes feast on many oil reservoirs, but it has been unclear how the micro-organisms got to those locales. One proposal has been that the microbes colonize a pool of dead algae corpses and then go along for the ride as the pool gets buried deeper and deeper and the algae slowly become oil. That’s the so-called "burial and isolation" hypothesis.

But under that set of rules each pool of oil should have its own unique microbes—and that's not the case, according to a recent study in the Journal of the International Society for Microbial Ecology. [Camilla L. Nesbø et al, Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments]

Researchers surveyed the genetics of oil-eating microbes from around the world. They found that populations from Nevada to the North Sea matched up almost exactly. They also determined that microbes in the North Sea appear to have swapped genes with Japanese microbes despite the locations being more than 8,000 kilometers apart on the Earth’s surface. 

These findings suggest that the deep biosphere is actually filled with connections, and that microbes move from one oil reservoir to another, colonizing them almost as soon as they form in some cases. Or it could also be that marine microbes migrate down and then evolutionary selection pressure causes a convergence in the genetics that make it possible to survive under these extreme conditions. 


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Scientists link unexplained childhood paralysis to enterovirus D68

Scientists link unexplained childhood paralysis to enterovirus D68 | WWWBiology | Scoop.it

A research team led by UC San Francisco scientists has found the genetic signature of enterovirus D68 (EV-D68) in half of California and Colorado children diagnosed with acute flaccid myelitis -- sudden, unexplained muscle weakness and paralysis -- between 2012 and 2014, with most cases occurring during a nationwide outbreak of severe respiratory illness from EV-D68 last fall. The finding strengthens the association between EV-D68 infection and acute flaccid myelitis, which developed in only a small fraction of those who got sick. The scientists could not find any other pathogen capable of causing these symptoms, even after checking patient cerebrospinal fluid for every known infectious agent.


Researchers analyzed the genetic sequences of EV-D68 in children with acute flaccid myelitis and discovered that they all corresponded to a new strain of the virus, designated strain B1, which emerged about four years ago and had mutations similar to those found in poliovirus and another closely related nerve-damaging virus, EV-D70. The B1 strain was the predominant circulating strain detected during the 2014 EV-D68 respiratory outbreak, and the researchers found it both in respiratory secretions and -- for the first time -- in a blood sample from one child as his acute paralytic illness was worsening.


The study also included a pair of siblings, both of whom were infected with genetically identical EV-D68 virus, yet only one of whom developed acute flaccid myelitis. 


"This suggests that it's not only the virus, but also patients' individual biology that determines what disease they may present with," said Charles Chiu, MD, PhD, an associate professor of Laboratory Medicine and director of UCSF-Abbott Viral Diagnostics and Discovery Center. "Given that none of the children have fully recovered, we urgently need to continue investigating this new strain of EV-D68 and its potential to cause acute flaccid myelitis."


Among the 25 patients with acute flaccid myelitis in the study, 16 were from California and nine were from Colorado. Eleven were part of geographic clusters of children in Los Angeles and in Aurora, Colorado, who became symptomatic at the same time, and EV-D68 was detected in seven of these patients.


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Mammoth genome sequence completed

Mammoth genome sequence completed | WWWBiology | Scoop.it

An international team of scientists has sequenced the complete genome of the woolly mammoth. A US team is already attempting to study the animals' characteristics by inserting mammoth genes into elephant stem cells. They want to find out what made the mammoths different from their modern relatives and how their adaptations helped them survive the ice ages.


The new genome study has been published in the journal Current Biology. Dr Love Dalén, at the Swedish Museum of Natural History in Stockholm, told BBC News that the first ever publication of the full DNA sequence of the mammoth could help those trying to bring the creature back to life. "It would be a lot of fun (in principle) to see a living mammoth, to see how it behaves and how it moves," he said.


But he would rather his research was not used to this end. "It seems to me that trying this out might lead to suffering for female elephants and that would not be ethically justifiable."


Dr Dalén and the international group of researchers he is collaborating with are not attempting to resurrect the mammoth. But the Long Now Foundation, an organisation based in San Francisco, claims that it is. Now, with the publication of the complete mammoth genome, it could be a step closer to achieving its aim.

 

On its website, the foundation says its ultimate goal is "to produce new mammoths that are capable of repopulating the vast tracts of tundra and boreal forest in Eurasia and North America. "The goal is not to make perfect copies of extinct woolly mammoths, but to focus on the mammoth adaptations needed for Asian elephants to live in the cold climate of the tundra.


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Scientists watch live taste cells in action

Scientists watch live taste cells in action | WWWBiology | Scoop.it

Scientists have for the first time captured live images of the process of taste sensation on the tongue. The international team imaged single cells on the tongue of a mouse with a specially designed microscope system. "We've watched live taste cells capture and process molecules with different tastes," said biomedical engineer Dr Steve Lee, from the ANU Research School of Engineering.

 

There are more than 2,000 taste buds on the human tongue, which can distinguish at least five tastes: salty, sweet, sour, bitter and umami.However the relationship between the many taste cells within a taste bud, and our perception of taste has been a long standing mystery, said Professor Seok-Hyun Yun from Harvard Medical School. "With this new imaging tool we have shown that each taste bud contains taste cells for different tastes," said Professor Yun.

 

The team also discovered that taste cells responded not only to molecules contacting the surface of the tongue, but also to molecules in the blood circulation." We were surprised by the close association between taste cells and blood vessels around them," said Assistant Professor Myunghwan (Mark) Choi, from the Sungkyunkwan University in South Korea. "We think that tasting might be more complex than we expected, and involve an interaction between the food taken orally and blood composition," he said.


The team imaged the tongue by shining a bright infrared laser on to the mouse's tongue, which caused different parts of the tongue and the flavor molecules to fluoresce. The scientists captured the fluorescence from the tongue with a technique known as intravital multiphoton microscopy. They were able to pick out the individual taste cells within each taste bud, as well as blood vessels up to 240 microns below the surface of the tongue. The breakthrough complements recent studies by other research groups that identified the areas in the brain associated with taste.


The team now hopes to develop an experiment to monitor the brain while imaging the tongue to track the full process of taste sensation. However to fully understand the complex interactions that form our basic sense of taste could take years, Dr Lee said. "Until we can simultaneously capture both the neurological and physiological events, we can't fully unravel the logic behind taste," he said.


The research has been published in the latest edition of Nature Publishing Group's Scientific Reports


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CRISPR-CAS editing brings cloning of woolly mammoth one step closer to reality

CRISPR-CAS editing brings cloning of woolly mammoth one step closer to reality | WWWBiology | Scoop.it

A team of researchers working at Harvard University has taken yet another step towards bringing to life a reasonable facsimile of a woolly mammoth—a large, hairy elephant-like beast that went extinct approximately 3,300 years ago. The work by the team has not been published as yet, because as team lead George Church told The Sunday Times, recently, they believe they have more work to do before they write up their results.

 

Church is quick to point out that his team is not cloning the mammoth, instead they are rebuilding the genome of the ancient animal by studying its DNA, replicating it and then inserting the copy into the genome of an Asian elephant—the closest modern day equivalent. They are not bringing forth a new mammoth yet either—all of their work is confined to simple cells in their lab. What they have done, however, is build healthy living elephant cells with mammoth DNA in them. Their work is yet another step towards that ultimate goal, realizing the birth of a wooly mammoth that is as faithful to the original as is humanly possible.


Talk of cloning a mammoth began not long after scientists learned how to actually do cloning—mammoth carcasses have been found in very cold places which preserved remains, which of course, included DNA. But not everyone has been onboard with the idea—some claim it is stepping into God's territory, others suggest it seems ridiculous considering all of the species that are nearing extinction, including those of elephants. Why not use those financial resources that are now going towards bringing back something that has gone extinct, to saving those that are still here?


The technique the team is using is called Crispr, it allows for reproducing exact copies of genes—in this case 14 mammoth genes, which are then inserted into elephant genes. As Church explains, the team prioritizes which genes are replicated and inserted, based on such factors as hairiness, ear size, and subcutaneous fat, which the animal needed to survive in its harsh cold environment.


Not clear as yet is when or if the team at Harvard has plans to produce an actual living mammoth, or if they will leave that to other teams working on similar projects.


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Praveen Senaratne's curator insight, March 26, 5:31 AM

What these researchers tend to achieve is amazing. The woolly mammoth is the great ancestors of the modern elephants and was a magnificent mammal. To bring to like a reasonable facsimile is an extraordinary task. Personally I would love to pursue a career as a researcher and in the future I hope technology helps to further improve the work of researchers.  

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Giant ancient amphibian was bigger than a human

Giant ancient amphibian was bigger than a human | WWWBiology | Scoop.it

Before dinosaurs came along, one of Earth’s top predators was a salamander-like amphibian that lived in tropical areas of the supercontinent Pangaea. Fossils unearthed from a 30- to 40-centimeter-thick bone bed in southern Portugal suggest the creature was more than 2 meters long, weighed as much as 100 kilograms, and had a broad flat head the size and shape of a toilet seat. The newly described species (artist's representation shown), which lived between 220 million and 230 million years ago, was one of the largest in a group of amphibians known as metoposaurs and is the first known in this region from well-preserved fossils, the researchers report online today in the Journal of Vertebrate Paleontology.


The species has been dubbed Metoposaurus algarvensis to honor the Algarve region of Portugal, where the fossils were unearthed. (Even though the genus name contains the Greek word saur, which translates as “lizard,” these creatures and their kin were amphibians.) The 4-square-meter area of the bone bed already excavated has yielded 10 skulls and hundreds of remains, suggesting that the creatures became concentrated in one area and then died when the lake they inhabited dried up, the researchers say. Because the beasts had spindly limbs probably insufficient to support their weight, they likely remained in the water most of the time, feeding on fish but possibly snacking on small ancestors of dinosaurs or mammals that wandered too near the waterside. Similar bone beds that include other species of metoposaurs have been found in what are now Africa, Europe, and North America—a hint that climate at the time was highly unpredictable and prone to lengthy droughts.


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Fecal transplants successful for treating C. difficile infection

Fecal transplants successful for treating C. difficile infection | WWWBiology | Scoop.it

Distasteful as it sounds, the transplantation of fecal matter is more successful for treating Clostridium difficile infections than previously thought. The research, published in the open access journal Microbiome, reveals that healthy changes to a patient's microbiome are sustained for up to 21 weeks after transplant, and has implications for the regulation of the treatment.


Clostridium difficile infections are a growing problem, leading to recurrent cases of diarrhea and severe abdominal pain, with thousands of fatalities worldwide every year. The infection is thought to work by overrunning the intestinal microbiome - the ecosystem of microorganisms that maintain a healthy intestine.


Fecal microbiota transplantation was developed as a method of treating C. difficile infection, and is particularly successful in patients who suffer repeat infections. Fecal matter is collected from a donor, purified, mixed with a saline solution and placed in a patient, usually by colonoscopy.


Previous research has shown that the fecal microbiota of patients resembles that of the donor, but not much is known about the short and long term stability of fecal microbiota transplanted into recipients.

In this research, Michael Sadowsky and colleagues at the University of Minnesota collected fecal samples from four patients before and after their fecal transplants. Three patients received freshly prepared microbiota from fecal matter and one patient received fecal microbiota that had previously been frozen. All received fecal microbiota from the same pre-qualified donor.


The team compared the pre- and post-transplant fecal microbial communities from the four patients, as well as from 10 additional patients with recurring C. difficile infections, to the sequences of normal subjects described in the Human Microbiome Project. In addition, they looked at the changes in fecal bacterial composition in recipients over time, and compared this to the changes observed within samples from the donor.


Surprisingly, after transplantation, patient samples appeared to sustain changes in their microbiome for up to 21 weeks and remained within the spectrum of fecal microbiota characterized as healthy.


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Imaging the 3D structure of a single virus using the world's most powerful x-ray free-electron laser

Imaging the 3D structure of a single virus using the world's most powerful x-ray free-electron laser | WWWBiology | Scoop.it

By measuring a series of diffraction pattern from a virus injected into an XFEL beam, researchers at Stanford’s Linac Coherent Light Source (LCLS) have determined the first three-dimensional structure of a virus, using a mimivirus.


X-ray crystallography has solved the vast majority of the structures of proteins and other biomolecules. The success of the method relies on growing large crystals of the molecules, which isn’t possible for all molecules.


“Free-electron lasers provide femtosecond X-ray pulses with a peak brilliance ten billion times higher than any previously available X-ray source,” the researchers note in a paper inPhysical Review Letters. “Such a large jump in one physical quantity is very rare, and can have far reaching implications for several areas of science. It has been suggested that such pulses could outrun key damage processes and allow structure determination without the need for crystallization.”


The current resolution of the technique (about 100 nanometers) would be sufficient to image important pathogenic viruses like HIV, influenza and herpes, and further improvements may soon allow researchers to tackle the study of single proteins, the scientists say.

 

Mimivirus is one of the largest known viruses. The viral capsid is about 450 nanometers in diameter and is covered by a layer of thin fibres. A 3D structure of the viral capsid exists, but the 3D structure of the inside was previously unknown.


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Radical Vaccine Design Effective Against Herpes Viruses

Radical Vaccine Design Effective Against Herpes Viruses | WWWBiology | Scoop.it

Herpes simplex virus infections are an enormous global health problem and there is currently no viable vaccine. For nearly three decades, immunologists’ efforts to develop a herpes vaccine have centered on exploiting a single protein found on the virus’s outer surface that is known to elicit robust production of antibodies. Breaking from this approach, Howard Hughes Medical Institute (HHMI) scientists at Albert Einstein College of Medicine have created a genetic mutant lacking that protein. The result is a powerfully effective vaccine against herpes viruses.


“We have a very promising new candidate for herpes,” says William Jacobs, an HHMI investigator at the Albert Einstein College of Medicine, “but this might also be a good candidate as a vaccine vector for other mucosal diseases, particularly HIV and tuberculosis.”


The new vaccine was found to be effective against the two most common forms of herpes that cause cold sores (HSV-1) and genital ulcers (HSV-2). Both are known to infect the body’s nerve cells, where the virus can lay dormant for years before symptoms reappear. The new vaccine is the first to prevent this type of latent infection. “With herpes sores you continually get them,” Jacobs says. “If our vaccine works in humans as it does in mice, administering it early in life could completely eliminate herpes latency.” Jacobs and his colleagues reported their findings on March 10, 2015, in the journal eLife.


HSV-2 is a lifelong, incurable infection that causes recurrent and painful genital sores and increases susceptibility to HIV. Also, babies born to mothers with active genital herpes have a more than 80 percent mortality rate. Current estimates suggest that 500 million people worldwide are infected with HSV-2, with approximately 20 million new cases occurring annually. While infection rates in the U.S. hover around 15 to 20 percent, HSV-2 is highly prevalent in sub-Saharan Africa, where nearly three in four women have contracted the virus, contributing significantly to the region’s HIV epidemic.


The related virus, HSV-1 is primarily associated with oral lesions, but is a major cause of corneal blindness and infects around 60 percent of the world’s population. Notably, HSV-1 has been increasingly recognized as a cause of genital herpes in the United States and other developed countries.

 
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Humans toss 8 million metric tons of plastic into the ocean pro year, study shows

Humans toss 8 million metric tons of plastic into the ocean pro year, study shows | WWWBiology | Scoop.it

Scientists for decades have been worried about plastic clogging up our oceans, but now they finally know just how bad the problem is. We dump about five shopping bags full of plastic for every foot of coastline in the world every year, according to a new study. The numbers are orders of magnitude higher than prior estimates.


If we continue to produce large amounts of plastic—and can’t find a better way to dispose of them—the amount of plastic in our oceans will double over the next decade, according to Jenna Jambeck, an environmental engineer at the University of Georgia and lead author on the study.

 

She says these numbers actually undercount the problem because they account for only floating plastic. As much as 50 percent of the plastic produced in North America probably sinks to the ocean floor, she says.

The 8 million metric tons of plastic that litters our oceans every year consists of not only the usual suspects (like six-pack plastic rings, which are the bane of sea turtles), but also microplastics, tiny bits of debris smaller than your fingernail. Microplastics endanger marine life of all sizes, from whales to barnacles, as they are easy to swallow and may contain dangerous chemicals.

 

Jambeck and her team noticed at least one recurring theme within the data. Middle-income countries, especially those that have begun to industrialize but have not yet figured out how to manage their waste, end up tossing a lot of garbage in their oceans. One outlier is the United States, a rich country that would seem to have its waste management act together but still dumps a lot of plastic into the oceans.



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Parasite creating deformed frogs with up to 10 legs in the Western U.S.

Parasite creating deformed frogs with up to 10 legs in the Western U.S. | WWWBiology | Scoop.it
A flatworm parasite called Ribeiroia ondatrae infects several species of frogs just as they're developing their limbs, causing an assortment of defects such as no legs or even multiple legs that jut out at weird angles from the frogs' bodies scientists say.

 

Watch a video of the deformed frogs.

 

The deformed frogs are often unable to move and either die or quickly get eaten by predators. Scientists already knew that the parasite was the culprit in the frog malformations, but the researchers wanted to find out whether known hot spots of Ribeiroia populations in four western states had changed since they were last surveyed in 1999. So in 2010 Pieter Johnson, an ecologist at the University of Colorado at Boulder, and colleagues gathered data on frogs and parasites in 48 wetlands in California, Oregon, Washington, and Montana.


The Ribeiroia parasite has a complex, multihost life cycle, which begins with the ramshorn snail, a creature common to many western U.S wetlands. The flatworm asexually clones itself inside the snail, stripping the mollusk of its gonads and converting it into a "parasite machine," Johnson said. Each night the snail releases hundreds of free-swimmingRibeiroia larvae, which seek out their next hosts—tadpoles—with "remarkable precision."


The parasite larvae penetrate the tadpoles' tissue and zero in on the developing limb buds, so that when a tadpole begins to metamorphose into a frog, its "primary system of locomotion doesn't work—it can't jump, can't swim," he said. "That's when the birds"—the parasite's final host—"zoom in and eat the young mutated frogs up like popcorn."


The parasite then reproduces sexually inside the birds, and when the birds defecate, their feces contain parasite eggs that eventually make their way back into the snails.


Though the Ribeiroia parasite occurs naturally in North America, human activities likely have something to do with its prevalence, Johnson noted. For instance, the snails feed on algae, and runoff from agriculture and industry into wetlands contains nutrients that act as fertilizer, boosting algae growth. With more snails in the wetlands, the parasites have more initial hosts to infect, Johnson noted.


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Why are 10% of the world population left-handed? What are the advantages / disadvantages?

Why are 10% of the world population left-handed? What are the advantages / disadvantages? | WWWBiology | Scoop.it

Today, about one-tenth of the world’s population are southpaws. Why are such a small proportion of people left-handed -- and why does the trait exist in the first place? Daniel M. Abrams investigates how the uneven ratio of lefties and righties gives insight into a balance between competitive and cooperative pressures on human evolution.


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New silicone infused with silicone oil: Super-slippery, and proven to keep bacteria from growing on medical tubing

New silicone infused with silicone oil: Super-slippery, and proven to keep bacteria from growing on medical tubing | WWWBiology | Scoop.it

Infusing liquids into polymers makes long lasting, self-replenishing material that repels deadly bacterial build-up. Harvard researchers have demonstrated a powerful, long-lasting, repellent surface technology that can be used with medical materials to prevent infections caused by microbial biofilms.

 

More than 80 percent of microbial infections in the human body are caused by a build-up of bacteria, according to the National Institutes of Health (NIH). Bacteria cells gain a foothold in the body by accumulating and forming into adhesive colonies called biofilms, which help them to thrive and survive but cause often serious infections and associated life-threatening risks to their human hosts. These biofilms commonly form on medical surfaces including those of mechanical heart valves, urinary catheters, intravenous catheters, and other implants. But a new study reported a powerful, long-lasting repellent surface technology that can be used with medical material to prevent these kind of infections caused by biofilms. The new approach, which its inventors are calling "liquid-infused polymers", joins an arsenal of slippery and hydrophobic surface coatings that have been developed at Harvard's School of Engineering and Applied Sciences (SEAS) and the Wyss Institute for Biologically Inspired Engineering.


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