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Scooped by Dr. Stefan Gruenwald!

Novel smaller Cas9 enzyme moves CRISPR gene editing closer to the clinic

Novel smaller Cas9 enzyme moves CRISPR gene editing closer to the clinic | Amazing Science |
A tweak to a technique that edits DNA with pinpoint precision has boosted its ability to correct defective genes in people. Called CRISPR, the method is already used in the lab to insert and remove genome defects in animal embryos. But the genetic instructions for the machinery on which CRISPR relies — a gene-editing enzyme called Cas9 and RNA molecules that guide it to its target — are simply too large to be efficiently ferried into most of the human body’s cells. This week, researchers report a possible way around that obstacle: a Cas9 enzyme that is encoded by a gene about three-quarters the size of the one currently used. The finding, published on 1 April in Nature, could open the door to new treatments for a host of genetic maladies (F. A. Ran et al. Nature; 2015).

“There are thousands of diseases in humans associated with specific genetic changes,” says David Liu, a chemical biologist at Harvard University in Cambridge, Massachusetts, who was not involved in the latest study. “A fairly large fraction of those have the potential to be addressed using genome editing.”

Genome editing has generated controversy, with unconfirmed reports of its use in human embryos. Some scientists have expressed concern that the technique might be used by fertility doctors to edit the genes of human embryos before its safety is established (see also E. Lanphier et al. Nature 519, 410–411; 2015). That concern is exacerbated by the fact that changes made by the procedure in embryos would be passed to all subsequent generations without giving anyone affected the opportunity to consent (see Nature 519, 272; 2015). But in the non-reproductive cells of children and adults, where inter­generational issues are not a concern, researchers and companies are already racing to develop CRISPR as a clinical tool.

The ethics of that pursuit may be more straightforward, but its execution can be harder than using CRISPR in embryos. An embryo consists of a small number of cells that give rise to a human. To edit the genome at that stage is simply a matter of injecting the necessary CRISPR components into a few cells. An adult human, however, is a mix of trillions of cells assembled into many different tissues. Researchers fret over how to target the CRISPR machinery to the specific cells where defective genes are disrupting physiological processes.

“You can have the most optimal gene-editing system in the world, but if you can’t deliver it to the proper cell type, it’s irrelevant,” says Nessan Bermingham, chief executive of Intellia Therapeutics in Cambridge, Massachusetts, which aims to bring genome editing to the clinic. “We’re spending a tremendous amount of time working on it.”  Gene-therapy researchers often harness a virus called AAV to shuttle foreign genes into mature human cells. However, most laboratories use a gene encoding the Cas9 protein that is too large to fit in the snug confines of the AAV genome alongside the extra sequences necessary for Cas9 function.

Feng Zhang of the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, and his colleagues decided to raid bacterial genomes for a solution, because the CRISPR system is derived from a process that bacteria use to snip unwanted DNA sequences out of their genomes. Zhang’s team analysed genes encoding more than 600 Cas9 enzymes from hundreds of bacteria in search of a smaller version that could be packaged in AAV and delivered to mature cells.

The gene encoding Cas9 in Staphylococcus aureus — a bacterium best known for causing skin infections and food poisoning — was more than 1,000 DNA letters smaller than the one for the commonly used Cas9. The researchers packed it into AAV along with RNAs that would target the enzyme to modify a cholesterol regulatory gene in the liver. Within a week of injecting mice with the modified virus, the team found that more than 40% of liver cells contained the modified gene. “It’s a terrific addition to the set of tools that genome engineers have at their disposal,” says Liu. He has been developing ways to transport the larger Cas9 protein, bound to its guide RNAs, into cells without relying on a virus. Bermingham says that he expects labs to develop multiple delivery mechanisms that are tailored to individual tissues.

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Fish Oil Claims are Not Supported by Research Studies

Fish Oil Claims are Not Supported by Research Studies | Amazing Science |

Fish oil is now the third most widely used dietary supplement in the United States, after vitamins and minerals, according to a recent report from the National Institutes of Health. At least 10 percent of Americans take fish oil regularly, most believing that the omega-3 fatty acids in the supplements will protect their cardiovascular health. But there is one big problem: The vast majority of clinical trials involving fish oil have found no evidence that it lowers the risk of heart attack and stroke.

From 2005 to 2012, at least two dozen rigorous studies of fish oil were published in leading medical journals, most of which looked at whether fish oil could prevent cardiovascular events in high-risk populations. These were people who had a history of heart disease or strong risk factors for it, like high cholesterol, hypertension or Type 2 diabetes.

All but two of these studies found that compared with a placebo, fish oil showed no benefit. And yet during this time, sales of fish oil more than doubled, not just in the United States but worldwide, said Andrew Grey, an associate professor of medicine at the University of Auckland in New Zealand and the author of a 2014 study on fish oil in JAMA Internal Medicine.

“There’s a major disconnect,” Dr. Grey said. “The sales are going up despite the progressive accumulation of trials that show no effect.”

In theory at least, there are good reasons that fish oil should improve cardiovascular health. Most fish oil supplements are rich in two omega-3 fatty acids — eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) — that can have a blood-thinning effect, much like aspirin, that may reduce the likelihood of clots. Omega-3s can also reduce inflammation, which plays a role in atherosclerosis. And the Food and Drug Administration has approved at least three prescription types of fish oil — Vascepa, Lovaza and a generic form — for the treatment of very high triglycerides, a risk factor for heart disease.

But these properties of omega-3 fatty acids have not translated into notable benefits in most large clinical trials.

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Chimp Eggs Die Off Later than Humans Eggs — Even Though Humans Live Longer

Chimp Eggs Die Off Later than Humans Eggs — Even Though Humans Live Longer | Amazing Science |

The oocytes (eggs) of chimpanzees degrade at a slower rate than the oocytes of women, even though chimps do not live as long. Indeed, many chimpanzees can get pregnant while in the thralls of geriatric diseases, unlike women, according to a recent Age study by Kristen Hawkes.

This new information offers more fuel for a theory called the Grandmother Hypothesis, which holds that women undergo menopause for an adaptive evolutionary reason, not just because humans are living longer and the ovaries haven’t caught up.

“In the other living hominids, the great apes, both cycling physiology and everything else senesce together,” Hawkes told Bioscience Technology. “As those things separate in our lineage, there have to be consequences for the interaction between the ovaries and physiology in general.”  As Hawkes' group noted in the recent paper, anthropologists “should have expected something tricky here. The ovaries are not ever operating on their own.  The HPO (hypothalamic pituitary gonadal) axis—where there are key interactions between the ovaries and brain—has to behave differently in the perimenopausal years in us vs chimpanzees.”

Weill Cornell Medical College reproductive medicine researcher Roger Gosden has noted that a woman’s reproductive system ages faster than her other organs to the point where, by age 45,  it is essentially 80 years old. The vast majority of animals do not experience any menopause, let alone the length experienced by women.

Biologist G.C. Williams was first to propose that this long menopause might be an adaptation. He posited that it may have turned out to be an evolutionary advantage for older, frailer women to stop dividing their declining energies between nurturing existing children and preparing for new ones, and simply focusing on the children they had.  Since women’s dependent and in-utero children often die when they do, older mothers would stop risking their lives, and those of their children, if they stopped being fertile early on, avoiding risky older childbirths.

Hawkes has expanded greatly on the theory, suggesting that grandmothers became critical for survival when humans switched to a more difficult tuber diet (requiring vigorous female foraging and digging) during the Pleistocene climate change 1.8 million years ago. Grandmotherly tuber-digging shifts let mothers have many children, and focus on nurturing not food-gathering. Furthermore, Hawkes believes all this may have contributed to our bigger brains, as larger families meant more competition for mothers’ and grandmothers’ attention. So more communication ensued.

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This remarkable new exoskeleton slips on like a boot and makes your walking more efficient

This remarkable new exoskeleton slips on like a boot and makes your walking more efficient | Amazing Science |

The latest exoskeleton technology doesn't need an outside power source to boost your strength. It harnesses the power of your own muscles to put a spring in your step instead. And soon baby boomers could be using it to keep hiking and jogging just a few years longer.

The new devices, described Wednesday in Nature, are still just in the prototype phase. But the researchers who created the inexpensive, easy-to-wear exoskeletons believe they could be ubiquitous in another decade. They're quite unlike the hulking, "Iron Man"-like suits that others have created to help people walk more easily. These little braces don't require any outside power, and they make walking 7 percent more efficient with nothing but a well-placed spring system. They can't support someone who can't stand on her own like a bulkier, motor-aided suit might. But for people who can walk but have difficulty doing so, the boot-like new apparatus could help create a more balanced, comfortable gait.

Just under 10 percent less energy per step doesn't sound like much -- it's the equivalent of removing a 10-pound backpack. According to study co-author Gregory Sawicki, a biomedical engineer and locomotion physiologist in the joint NC State/University of North Carolina-Chapel Hill Department of Biomedical Engineering, people using the braces don't really notice the difference -- until it's gone.

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Researchers build a robot that can reproduce

Researchers build a robot that can reproduce | Amazing Science |
One of the dreams of both science fiction writers and practical robot builders has been realized, at least on a simple level: Cornell University researchers have created a machine that can build copies of itself.

Admittedly the machine is just a proof of concept -- it performs no useful function except to self-replicate -- but the basic principle could be extended to create robots that could replicate or at least repair themselves while working in space or in hazardous environments, according to Hod Lipson, Cornell assistant professor of mechanical and aerospace engineering, and computing and information science, in whose lab the robots were built and tested.

Lipson and colleagues report on the work in a brief communication in the May 12 issue of Nature.

Their robots are made up of a series of modular cubes -- called "molecubes" -- each containing identical machinery and the complete computer program for replication. The cubes have electromagnets on their faces that allow them to selectively attach to and detach from one another, and a complete robot consists of several cubes linked together. Each cube is divided in half along a long diagonal, which allows a robot composed of many cubes to bend, reconfigure and manipulate other cubes. For example, a tower of cubes can bend itself over at a right angle to pick up another cube.

Although these experimental robots work only in the limited laboratory environment, Lipson suggests that the idea of making self-replicating robots out of self-contained modules could be used to build working robots that could self-repair by replacing defective modules. For example, robots sent to explore Mars could carry a supply of spare modules to use for repairing or rebuilding as needed, allowing for more flexible, versatile and robust missions. Self-replication and repair also could be crucial for robots working in environments where a human with a screwdriver couldn't survive.To begin replication, the stack of cubes bends over and sets its top cube on the table. Then it bends to one side or another to pick up a new cube and deposit it on top of the first. By repeating the process, one robot made up of a stack of cubes can create another just like itself. Since one robot cannot reach across another robot of the same height, the robot being built assists in completing its own construction.
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‘Nanoneedles’ generate new blood vessels in mice, paving the way for new regenerative medicine

‘Nanoneedles’ generate new blood vessels in mice, paving the way for new regenerative medicine | Amazing Science |
Scientists have developed “nanoneedles” that have successfully prompted parts of the body to generate new blood vessels, in a trial in mice.

The researchers, from Imperial College London and Houston Methodist Research Institute in the USA, hope their nanoneedle technique could ultimately help damaged organs and nerves repair themselves and help transplanted organs  thrive.

In a trial described in Nature Materials, the team showed they could deliver nucleic acids DNA and siRNA to back muscles in mice. After seven days there was a six-fold increase in the formation of new blood vessels in the mouse back muscles, and blood vessels continued to form over a 14 day period.

The nanoneedles are tiny porous structures that act as a sponge to load significantly more nucleic acids than solid structures. This makes them more effective at delivering their payload. They can penetrate the cell, bypassing its outer membrane, to deliver nucleic acids without harming or killing the cell.

The nanoneedles are made from biodegradable silicon, meaning that they can be left in the body without leaving a toxic residue behind. The silicon degrades in about two days, leaving behind only a negligible amount of a harmless substance called orthosilicic acid.

The hope is that one day scientists will be able to help promote the generation of new blood vessels in people, using nanoneedles, to provide transplanted organs or future artificial organ implants with the necessary connections to the rest of the body, so that they can function properly with a minimal chance of being rejected.

“This is a quantum leap compared to existing technologies for the delivery of genetic material to cells and tissues,” said Ennio Tasciotti, Co-Chair, Department of Nanomedicine at Houston Methodist Research Institute and co-corresponding author of the paper.

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Almost too complex: Model to analyze miRNA-ceRNA interactions and validate them using synthetic gene circuits

Almost too complex: Model to analyze miRNA-ceRNA interactions and validate them using synthetic gene circuits | Amazing Science |

In the complex, somewhat rarified world of interactions between various flavors of RNA, one elusive goal is to understand the precise regulatory relationships between competing endogenous RNA (ceRNA), microRNA (miRNA), small interfering RNA (siRNA) and messenger RNA (mRNA).

To enter this world prepared, here's a quick overview:

  • Competing endogenous RNAs, which include mRNAs, transcribed pseudogenes, long noncoding RNAs (lncRNA), and circular RNA (circRNA), regulate other RNA transcripts by competing for shared microRNA
  • MicroRNA is a small non-coding RNA molecule containing about 22 nucleotides found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression
  • Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression
  • Pseudogenes are sections of a chromosome that are imperfect, dysfunctional copies of functional genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell
  • Long noncoding RNA (lncRNA) comprises a large and diverse class of transcribed RNA molecules with a length of more than 200 nucleotides that do not encode proteins, and whose expression is developmentally regulated and that can be tissue- and cell-type specific
  • Circular RNA (circRNA) is a type of gene regulating noncoding RNA which, unlike the better-known linear RNA, forms a covalently closed continuous loop and that have not been shown to code for proteins
  • Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 base pairs in length, that has many functions but is most notable in the RNA interference (RNAi) pathway where it interferes with the expression of specific genes with complementary nucleotide sequences

Recently, scientists at Tsinghua University, Beijing investigated competing endogenous RNAs cross-regulation by creating a computational model, using it to quantitatively describe a minimum ceRNA network, and experimentally validating their model's predictions by utilizing multifluorescent synthetic gene circuits in cultured human cells. They found that the ceRNA effect is affected by the abundance of miRNA and ceRNAs, the number and affinity of binding sites, and the mRNA degradation pathway determined by the degree of miRNA/mRNA complementarity (a mirror image-like property shared between two DNA or RNA sequences that allows DNA replication and transcription). The researchers state that their findings have the potential to increase understanding quantitative properties of gene regulatory systems, contribute to the development of better tools for cell-type specific microRNA occupancy rate prediction, and benefit synthetic biology or genetic engineering research using miRNA or ceRNA in building more predictive parts with better quantitative behaviors.

Discussing the paper that he, Prof. Zhen Xie and their colleagues published in Proceedings of the National Academy of Sciences, Prof. Xiaowo Wang tells that one of the main challenges the researchers faced was applying a model-guided synthetic biology approach to quantitatively analyze the behavior of miRNA-mediated ceRNA regulation. "In mammalian cells, each type of miRNA can interact with dozens to hundreds of target RNA species – including protein-coding mRNAs, long non-coding RNAs and recently-discovered circular RNAs." Moreover, he explains, each RNA species can also interact with multiple miRNA species through various miRNA regulatory elements, or MREs, and the complex interaction network of miRNAs and their target RNAs has been shown to allow indirect cross-regulation between different competing endogenous RNAs (ceRNAs) by sequestering shared miRNAs, which is essential for regulating many biological functions. "However," he points out, "natural microRNA-ceRNA networks are complex and hard to perturb, which makes it difficult to quantitatively understand the mechanism of miRNA-mediated ceRNA regulation. Thus, we decided to implement an artificial miRNA-ceRNA system by transfecting synthetic gene circuits into human HEK293 cells to simulate the behavior of ceRNA regulation."

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Researchers develop molecular DNA backbone of super-slim, bendable digital displays

Researchers develop molecular DNA backbone of super-slim, bendable digital displays | Amazing Science |

From smart phones and tablets to computer monitors and interactive TV screens, electronic displays are everywhere. As the demand for instant, constant communication grows, so too does the urgency for more convenient portable devices -- especially devices, like computer displays, that can be easily rolled up and put away, rather than requiring a flat surface for storage and transportation.

A new Tel Aviv University study, published recently in Nature Nanotechnology ("Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson–Crick base pairing"), suggests that a novel DNA-peptide structure can be used to produce thin, transparent, and flexible screens. The research, conducted by Prof. Ehud Gazit and doctoral student Or Berger of the Department of Molecular Microbiology and Biotechnology at TAU's Faculty of Life Sciences, in collaboration with Dr. Yuval Ebenstein and Prof. Fernando Patolsky of the School of Chemistry at TAU's Faculty of Exact Sciences, harnesses bionanotechnology to emit a full range of colors in one pliable pixel layer -- as opposed to the several rigid layers that constitute today's screens."

Our material is light, organic, and environmentally friendly," said Prof. Gazit. "It is flexible, and a single layer emits the same range of light that requires several layers today. By using only one layer, you can minimize production costs dramatically, which will lead to lower prices for consumers as well."

For the purpose of the study, a part of Berger's Ph.D. thesis, the researchers tested different combinations of peptides: short protein fragments, embedded with DNA elements which facilitate the self-assembly of a unique molecular architecture.

Peptides and DNA are two of the most basic building blocks of life. Each cell of every life form is composed of such building blocks. In the field of bionanotechnology, scientists utilize these building blocks to develop novel technologies with properties not available for inorganic materials such as plastic and metal."

Our lab has been working on peptide nanotechnology for over a decade, but DNA nanotechnology is a distinct and fascinating field as well. When I started my doctoral studies, I wanted to try and converge the two approaches," said Berger. "In this study, we focused on PNA - peptide nucleic acid, a synthetic hybrid molecule of peptides and DNA. We designed and synthesized different PNA sequences, and tried to build nano-metric architectures with them."

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New rotary motor found in Flavobacterium johnsoniae

New rotary motor found in Flavobacterium johnsoniae | Amazing Science |

Harvard researchers, probing the mystery of how some bacteria move across surfaces, have discovered a kind of rotary motor in the bacterium Flavobacterium johnsoniae. The finding came as Abhishek Shrivastava, a postdoctoral fellow working in the lab of Howard Berg, the Herchel Smith Professor of Physics and a professor of molecular and cellular biology, was investigating how many types of bacteria, including F. johnsoniaeare able to move without the aid of flagella or pili. The discovery is described in a recently published paper in Current Biology.

“If you look at the diversity of the bacterial world, there are many bacteria — including F. johnsoniae — that do not have flagella or pili, yet they move quite easily over surfaces, and travel long distances. This movement is called ‘bacterial gliding,’” Shrivastava said. “To move by this process, bacteria require a constant influx of energy. We wanted to find out how bacterial gliding takes place and what could be a motor for gliding.”

Though researchers had long observed bacterial gliding, the precise mechanics underlying the behavior remained a mystery.

The first clues came a few years ago, Shrivastava said, when researchers discovered that the rod-shaped Flavobacteria are actually bristling with tiny filaments, made up of a protein called SprB. These filaments are required for motility.

Shrivastava and others used an antibody “glue” to pin one of the filaments down to a glass plate and found that when they are held down, the cells pinwheel around the point of attachment. If a small, plastic bead were attached to the filament, they found that it would also rotate. The torque generated by the gliding motor was calculated to be large, and comparable to torque generated by motors that drive flagellar filaments.

Though not the only one found in nature — a similar motor powers the flagella found on bacteria like E. coli — the rotary motor discovered by Shrivastava and colleagues appears to be distinct from others. “If you look at the genome sequence of this bacterium, it does not have the genes that make the proteins used to build the flagellar motor,” Shrivastava said. “It could be that some of the components are similar, but we are probably looking at some novel proteins. So we want to understand what makes up the nuts and bolts of this motor.”

Going forward, Berg said, researchers still have many questions to answer. “The flagellar motor has about 20 different kinds of parts, from a drive shaft to a rotary bearing and a universal joint — that kind of machinery is in this bug, but we have no idea what that is. What we need to do now is somehow pull it out and understand the architecture of this motor.

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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 | Amazing Science |
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.

CineversityTV's curator insight, March 30, 2015 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, 2015 4:49 AM

,New advances in biomedical technology

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Female Brain State Maintained by DNA Methylation

Female Brain State Maintained by DNA Methylation | Amazing Science |

Differences in male and female rodent sexual behaviors are programmed during brain development, but how exactly this occurs is not clear. In the preoptic area (POA) of the brain—a region necessary for male sex behavior—the female phenotype results from repression of male-linked genes by DNA methylation, according to a study published today (March 30, 2015) in Nature Neuroscience.

There is very little known about how the brain is masculinized—and even less about how it is feminized—even though the question has been studied for more than 50 years, said Bridget Nugent, study author and now a postdoctoral fellow at the University of Pennsylvania. These sex differences in the brain are programmed toward the end of fetal development, through to one week after birth in rodents. In males, testicular hormones drive masculinization of the brain; this was thought to occur by direct induction of gene expression by hormone-associated transcription factors. Because a feminized brain occurred in the absence of ovarian hormone signals, most researchers assumed that the female brain and behavior was a sort of default state, programmed during development when no male hormones are present. But the downstream mechanisms of how hormones can modify gene expression were not previously known.

“This study reveals that DNA methylation plays an important role in regulating sexual differentiation,” said Nirao Shah, who also studies the neural basis for sex-specific behaviors at the University of California, San Francisco, but was not involved with the work.

“Our understanding that the female state of the brain is the default still stands. What changes now, because of this study, is our thinking as to how the default state is preserved,” said Geert de Vries, director of the Neuroscience Institute at Georgia State University who studies how sex influences the developing brain but was not involved in the work. “The authors show that there is active repression of the masculine brain program, and that is really a novel idea.”

In other words, male hormones unleash the male program. “It’s an emancipation, you might say, of these genes that are suppressed by the female. So, evolutionarily, this evolved a lot differently than we thought,” said study author Margaret McCarthy, a professor of pharmacology at the University of Maryland School of Medicine.

Nugent, McCarthy, and their colleagues demonstrated that activity of DNA methyltransferase (Dnmt) enzymes—which control the methylation of DNA, and therefore gene repression—was lower in the POA of the brain in male versus female rats during the sensitive period. Treating newborn female rats with male hormones resulted in male-level Dnmt activity, but had no effect on older rats. Typical female rats also had twice the levels of fully methylated CpG sites throughout their genomes compared to either male or masculinized female rats.

The team was then able to drive both male morphology within the POA and male copulation behavior in female rats by administering small molecule inhibitors of Dnmts directly into the brain at birth.

While giving male hormones to females only modified female rodent sexual behavior during the critical period, inhibiting Dnmts led to a male phenotype even after the sensitive window had closed, 10 days after birth. The researchers also found that knocking out one of the Dnmt enzymes in a mouse model several days after birth—outside of the sensitive development window—resulted in female mice exhibiting male copulation behaviors.

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Plant virus can help you boil water 3x faster

Plant virus can help you boil water 3x faster | Amazing Science |

Scientists have found a way to boil water faster. The technology works by coating a heating element with a virus found on tobacco plants. The coating dramatically reduces the size and number of bubbles that form around the element as it gets warmer. Air pockets caused by bubbles temporarily insulate heating elements from the surrounding water, slowing down the transfer of heat. A coating made from the tobacco virus tripled the efficiency of boiling water, scientists said, which could save vast quantities of energy in industrial power plants or large-scale electronic cooling systems.

“Even slight improvements to technologies that are used so widely can be quite impactful,” said Matthew McCarthy, an engineer at Drexel University in Pennsylvania. Controlling the formation of bubbles would also help guard against a scenario called “critical heat flux” that is undesirable – sometimes disastrous – in industrial boilers. This happens when so many bubbles are forming that they merge into a blanket surrounding the element, meaning that it can no longer transfer heat to the water.

“What happens then is the dry surface gets hotter and hotter, like a pan on the stove without water in it,” said McCarthy. “This failure can lead to the simple destruction of electronic components, or in power plant cooling applications, the catastrophic meltdown of a nuclear reactor.” To counteract this effect, scientists have been attempting to develop surfaces that repel bubbles and keep the boiling surface wet. McCarthy’s team has identified tobacco mosaic virus, which is roughly pencil-shaped, as the perfect structure for wicking moisture downwards towards a surface.

The team has developed a genetically modified strain of the virus, with “molecular hooks” allowing it to adhere to nearly any surface. The researchers grow tobacco plants in the lab and infect them with the modified tobacco mosaic virus. “When the plants are really sick, we put them in the blender and you get a sort of green soup,” said McCarthy.

After several rounds of centrifuging and chemical separation, which takes two days, the scientists are left with a perfectly clear solution of concentrated virus. When poured over a surface, the virus self-assembles into a layer of nano-tendrils, each pointing upward like a blade of grass.

Naif Almalki's curator insight, March 30, 2015 5:00 AM

فيروس يساعد على تسريع غليان الماء ويحفظ الطاقة !

JIIP's curator insight, April 12, 2015 7:58 PM


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Designer's toolkit for dynamic DNA: Arm-waving nanorobot signals new flexibility in DNA origami

Designer's toolkit for dynamic DNA: Arm-waving nanorobot signals new flexibility in DNA origami | Amazing Science |

The latest DNA nanodevices created at the Technische Universitaet Muenchen (TUM) - including a robot with movable arms, a book that opens and closes, a switchable gear, and an actuator - may be intriguing in their own right, but that's not the point. They demonstrate a breakthrough in the science of using DNA as a programmable building material for nanometer-scale structures and machines. Results published in the journalScience reveal a new approach to joining - and reconfiguring - modular 3D building units, by snapping together complementary shapes instead of zipping together strings of base pairs. This not only opens the way for practical nanomachines with moving parts, but also offers a toolkit that makes it easier to program their self-assembly.

The field popularly known as "DNA origami," in reference to the traditional Japanese art of paper folding, is advancing quickly toward practical applications, according to TUM Prof. Hendrik Dietz. Earlier this month, Dietz was awarded Germany's most important research award, the Gottfried Wilhelm Leibniz Prize, for his role in this progress.

In recent years, Dietz and his team have been responsible for major steps in the direction of applications: experimental devices including a synthetic membrane channel made from DNA; discoveries that cut the time needed for self-assembly processes from a week to a few hours and enable yields approaching 100%; proof that extremely complex structures can be assembled, as designed, with subnanometer precision. Yet all those advances employed "base-pairing" to determine how individual strands and assemblies of DNA would join up with others in solution. What's new is the "glue."

"Once you build a unit with base pairs," Dietz explains, "it's hard to break apart. So dynamic structures made using that approach tended to be structurally simple." To enable a wider range of DNA nanomachines with moving parts and potentially useful capabilities, the team adapted two more techniques from nature's biomolecular toolkit: the way proteins use shape complementarity to simplify docking with other molecules, and their tendency to form relatively weak bonds that can be readily broken when no longer needed.

For the experiments reported in Science, Dietz and his co-authors took inspiration from a mechanism that allows nucleic acid molecules to bond through interactions weaker than base-pairing. In nature, weak bonds can be formed when the RNA-based enzyme RNase P "recognizes" so-called transfer RNA; the molecules are guided into close enough range, like docking spacecraft, by their complementary shapes.

The new technology from Dietz's lab imitates this approach. To create a dynamic DNA nanomachine, the researchers begin by programming the self-assembly of 3D building blocks that are shaped to fit together. A weak, short-ranged binding mechanism called nucleobase stacking can then be activated to snap these units in place. Three different methods are available to control the shape and action of devices made in this way.

What this has given us is a tiered hierarchy of interaction strengths," Dietz says, "and the ability to position - precisely where we need them - stable domains that can recognize and interact with binding partners." The team produced a series of DNA devices - ranging from micrometer-scale filaments that might prefigure technological "flagella" to nanoscale machines with moving parts - to demonstrate the possibilities and begin testing the limits.

For example, transmission electron micrographs of a three-dimensional, nanoscale humanoid robot confirm that the pieces fit together exactly as designed. In addition, they show how a simple control method - changing the concentration of positive ions in solution - can actively switch between different configurations: assembled or disassembled, with "arms" open wide or resting at the robot's side.

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Gynandromorphism: Half male, half female butterfly emerges

Gynandromorphism: Half male, half female butterfly emerges | Amazing Science |

Volunteers at the Academy of Natural Sciences of Drexel University were shocked when the above butterfly emerged from its chrysalis. “It slowly opened up, and the wings were so dramatically different, it was immediately apparent what it was,” Chris Johnson, a retired chemical engineer and museum volunteer, said in a statementThis Lexias pardalis butterfly is perfectly split down its middle -- with male coloring on the left side of its body and wings and female coloring on the right.

It's a condition called gynandromorphism. It usually happens early in development, when cells are just beginning to split to form an embryo. One of the early cells fails to split its sex chromosomes properly (for example, an XXYY might split into an X and an XYY instead of two XY cells). These cells continue to divide and proliferate, and they're signaling for the organism to grow into two different sexes.

Sometimes the gynandromorphism is "mosaic," meaning that the cells are spread throughout the body and not noticeable outwardly. And in some species, even being split down the middle ("bilateral" gynandromorphism) isn't all that noticeable, because males and females look alike.

That's why it's most commonly noticed in the insect world -- and especially in butterflies -- who have often evolved striking differences in color and shape based on sex.

“In most cases, such specimens are ‘discovered’ in museum collections by a researcher who is carefully examining reproductive organs of insects under the microscope and stumbles across a specimen with both male and female characteristics,” Entomology Collection Manager Jason Weintraub said in a statement.

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Atomic Hong-Ou-Mandel Experiment: Helium atoms put in same quantum state, start appearing in same place

Atomic Hong-Ou-Mandel Experiment: Helium atoms put in same quantum state, start appearing in same place | Amazing Science |

Quantum mechanics has so many counterintuitive features that it seems possible to learn a new one every month. Today's lesson involves particles that are set into the same quantum state and effectively become indistinguishable. Once they are indistinguishable, they start behaving that way, showing up in the same place even when we'd expect to see them distributed at random. In today's issue of Nature, a paper describes getting atoms to behave this way, blurring the lines between a quantum probability function and what we think of as a physical object.

The original issue of indistinguishability was highlighted in an experiment done decades ago using photons. Called the Hong, Ou, and Mandel experiment, it involved sending photons in the same quantum state into a partial mirror along two different paths. The partial mirror, called a beam splitter, has a 50/50 chance of reflecting a photon, shifting it from one path to the second.

Based on the 50/50 chance, you'd expect three different outcomes. Half the time, when the beamsplitter reflects neither or both of the photons, you'd expect one photon in each of the output paths. When the beamsplitter reflects only one photon, you'd see both photons in one or the other path (with a 25 percent chance for each).

But quantum mechanics has also shown that things like electrons and heavier particles—even molecules—can behave as waves when given the chance. So a team from Universite Paris Sud decided to try to replicate the Hong, Ou, and Mandel experiment with something a bit more substantial than a photon. They chose 4-helium atoms, which are relatively easy to set in an identical quantum state.

The experiment involved holding the atoms over a sensor using an optical trap. Because of the way the trap was set up, the atoms would start off moving upward at two different velocities until the influence of gravity started pulling them back downward. While they were moving upward, the atoms were hit with photons that would exchange their momenta. This causes them to cross paths before they begin to fall. At the precise point where the paths cross, the atoms were hit with photons again. But this time, the photons were only half the intensity, leading to a 50/50 chance that their momenta would change. In essence, this acted like a beam splitter for atoms.

As a result, the atoms became indistinguishable—within the experiment, we'd have no idea of when we'd expect them to impact the detector. Our classically trained expectations would predict a Gaussian (bell) curve, with momenta distributed around the two starting speeds (7 and 12 cm/sec) due to random error and noise. And that's similar to what the results look like. Except if you look at the correlations between when particles land, you see the same sort of bias that Hong, Ou, and Mandel saw: the atoms seem to show up at one or the other of the two speeds, but not both. Since they were indistinguishable, they acted that way and travelled together.

The behavior isn't perfect—there are more atoms traveling along both paths than we'd expect if the experiment were operating perfectly. But the authors ascribe the difference to experimental noise, and the team notes this behavior is still radically different from what classical mechanics would predict. And having gotten this to work with atoms, it's possible the technique could be expanded to work with larger particles, allowing us to probe the boundaries between the quantum and classical worlds.

Keith Wayne Brown's curator insight, April 3, 2015 11:28 AM

blurring the lines between probability and object

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Oxygen-depleted toxic oceans had key role in mass extinction over 200 million years ago

Oxygen-depleted toxic oceans had key role in mass extinction over 200 million years ago | Amazing Science |

Life of the Triassic met a choking end in a runaway greenhouse climate 200 million years ago, heating the seas into warm stagnation. The greenhouse was caused by CO2 released by massive outpourings of basalt from fissure eruptions associated with the opening of the Atlantic Ocean. The resulting boom in marine microbes consumed oxygen and released poisonous hydrogen sulfide into water and air, creating "dead zones" above and below, worldwide. Hydrogen sulfide posioning is detected by molecular fossils used as biomarkers.

The study, published in the upcoming edition of Geology, reveals that a condition called 'marine photic zone euxinia' took place in the Panathalassic Ocean- the larger of the two oceans surrounding the supercontinent of Pangaea.

Photic zone euxinia occurs when the sun-lit surface waters of the ocean become devoid of oxygen and are poisoned by hydrogen sulphide - a by-product of microorganisms that live without oxygen that is extremely toxic to most other lifeforms.

The international team of researchers studied fossilised organic molecules extracted from sedimentary rocks that originally accumulated on the bottom of the north-eastern Panthalassic Ocean, but are now exposed on the Queen Charlotte Islands, off the coast of British Columbia, Canada.

The team found molecules derived from photosynthesising brown-pigmented green sulphur bacteria - microorganisms that only exist under severely anoxic conditions - proving severe oxygen depletion and hydrogen sulphide poisoning of the upper ocean at the end of Triassic, 201 million years ago.

The researchers also documented marked changes in the nitrogen composition of organic matter, indicating that disruptions in marine nutrient cycles coincided with the development of low oxygen conditions.

Previous studies have reported evidence of photic zone euxinia from terrestrial and shallow, near-shore environments during the latest Triassic, but the new research is the first to provide such evidence from an open ocean setting, indicating these changes may have occurred on a global scale.

The University of Southampton's Professor Jessica Whiteside, who co-authored the study, explains: "As tectonic plates shifted to break up Pangaea, huge volcanic rifts would have spewed carbon dioxide into the atmosphere, leading to rising temperatures from the greenhouse effect. The rapid rises in CO2 would have triggered changes in ocean circulation, acidification and deoxygenation."

"These changes have the potential to disrupt nutrient cycles and alter food chains essential for the survival of marine ecosystems. Our data now provides direct evidence that anoxic, and ultimately euxinic, conditions severely affected food chains."

Lauri's curator insight, April 2, 2015 9:17 PM

Fueled by massive releases of CO2.

Preston McSwain's curator insight, May 4, 2015 9:22 AM

Don't let this happen again.  Clean Up Oceans

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Detection of Pathogens and Novel Viruses Carried by New York City Rats

Detection of Pathogens and Novel Viruses Carried by New York City Rats | Amazing Science |

No one was under the illusion that New York’s rats were clean creatures, but a study published this week in mBio found dozens of viruses that have never been described by science, some of which may be potentially harmful to humans. “While a subset of the agents we identified are known to cause disease in humans, many more are novel viruses whose zoonotic potential cannot be inferred from available data,” Cadhla Firth, the lead researcher of the team from Columbia University, wrote. “It is therefore possible that human infection with some of the agents identified here may already be occurring, and the risk of future zoonotic transmission should not be disregarded.”

Beyond that, the researchers found many, many pathogens that are well known and are very bad for people, pets, and sometimes even zebras. So, in an attempt to scare the bejesus out of everyone, I quickly analyzed the 32 species of clinically important microbes that were identified. 

Noah Harris's comment, September 3, 2015 9:27 PM
like not trying to piggyback off of James but i completely agree with him but i would like to know how are they useful in big city's cause if we really dont need them and if we dont then why do we keep them
Breanna Daniels's comment, September 23, 2015 5:50 PM
I honestly think that this is really bad. If the rats carry germs then it could kill a lot of people. It could spread and you never know if it could turn into a pandemic. I honestly think if we keep the streets clean it would make the world a whole lot better. Not saying it would kill all of the diseases but it would help preveNY Some Of Them. It would make it cleaner
Breanna Daniels's comment, September 23, 2015 5:50 PM
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Engineers create stretchable structures tougher than bulletproof vests

Engineers create stretchable structures tougher than bulletproof vests | Amazing Science |

Researchers at University of Texas at Dallas (UT Dallas) have created a material made from nanofibers that can stretch to up to seven times its length while remaining tougher than Kevlar. These structures absorb up to 98 joules per gram. Kevlar, often used to make bulletproof vests, can absorb up to 80 joules per gram. The researchers hope the structures will one day form material that can reinforce itself at points of high stress and could potentially be used in military airplanes or other defense applications.

In a study published by ACS Applied Materials and Interfaces, a journal of the American Chemical Society, researchers twisted nanofiber into yarns and coils. The electricity generated by stretching the twisted nanofiber formed an attraction ten times stronger than a hydrogen bond, which is considered one of the strongest forces formed between molecules.

Researchers sought to mimic their earlier work on the piezoelectric action (how pressure forms electric charges) of collagen fibers found inside bone in hopes of creating high-performance materials that can reinforce itself, said Dr. Majid Minary, an assistant professor of mechanical engineering in the University’s Erik Jonsson School of Engineering and Computer Science and senior author of the study.

“We reproduced this process in nanofibers by manipulating the creation of electric charges to result in a lightweight, flexible, yet strong material,” said Minary, who is also a member of the Alan G. MacDiarmid NanoTech Institute. “Our country needs such materials on a large scale for industrial and defense applications.”

Alberto Mazarro's curator insight, July 9, 2015 1:02 PM

El desarrollo y combinación de materiales compuestos con nanopartículas da propiedades impensables hasta hoy

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Earthlike ‘Star Wars’ Tatooines may be common in the Universe

Earthlike ‘Star Wars’ Tatooines may be common in the Universe | Amazing Science |

Luke Skywalker’s home in “Star Wars” is the desert planet Tatooine, with twin sunsets because it orbits two stars. So far, only uninhabitable gas-giant planets have been identified circling such binary stars, and many researchers believe rocky planets cannot form there. Now, mathematical simulations show that Earthlike, solid planets such as Tatooine likely exist and may be widespread.

“Tatooine sunsets may be common after all,” concludes the study by astrophysicists Ben Bromley of the University of Utah and Scott Kenyon of the Smithsonian Astrophysical Observatory.

“Our main result is that outside a small region near a binary star, [either rocky or gas-giant] planet formation can proceed in much the same way as around a single star,” they write. “In our scenario, planets are as prevalent around binaries as around single stars.”

The study has been submitted to Astrophysical Journal for review, but as is the custom in the field, the authors have posted the unreviewed paper on the scientific preprint website ArXiv.

The title of the new study is “Planet formation around binary stars: Tatooine made easy,” but the paper looks anything but easy: it is filled with mathematical formulas describing how binary stars can be orbited by planetesimals – asteroid-sized rocks that clump together to form planets.

“We took our sweet numerical time to show that the ride around a pair of stars can be just as smooth as around one,” when it comes to the early steps of planet formation, Bromley says. “The ‘made easy’ part is really saying the same recipe that works around the sun will work around Tatooine’s host stars.”

“For over a decade, astrophysicists believed that planets like Earth could not form around most binary stars, at least not close enough to support life,” he says. “The problem is that planetesimals need to merge gently together to grow. Around a single star, planetesimals tend to follow circular paths – concentric rings that do not cross. If planetesimals do approach each other, they can merge together gently.”

But if planetesimals orbit a pair of stars, “their paths get mixed up by the to-and-fro pull of the binary stars,” Bromley says. “Their orbits can get so tangled that they cross each other’s paths at high speeds, dooming them to destructive collisions, not growth.”

Previous research started with circular orbits when pondering planet formation around binary stars, Bromley says, while the new study shows that “planets, when they are small, will naturally seek these oval orbits and never start off on circular ones. … If the planetesimals are in an oval-shaped orbit instead of a circle, their orbits can be nested and they won’t bash into each other. They can find orbits where planets can form.”

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Shape-shifting frog discovered in the Ecuadorian Andes

Shape-shifting frog discovered in the Ecuadorian Andes | Amazing Science |

A frog in Ecuador's western Andean cloud forest changes skin texture in minutes, appearing to mimic the texture it sits on. Originally discovered by a Case Western Reserve University PhD student and her husband, a projects manager at Cleveland Metroparks' Natural Resources Division, the amphibian is believed to be the first known to have this shape-shifting capability.

The new frog is now officially called Pristimantis mutabilis, or mutable rainfrog. Colleagues working with the couple recently found that a known relative of the frog shares the same texture-changing quality--but it was never reported before.

The frogs are found at Reserva Las Gralarias, a nature reserve originally created to protect endangered birds in the Parish of Mindo, in north-central Ecuador.

The researchers, Katherine and Tim Krynak, and colleagues from Universidad Indoamérica and Tropical Herping (Ecuador) co-authored a manuscript describing the new animal and skin texture plasticity in the Zoological Journal of the Linnean Society. They believe their findings have broad implications for how species are and have been identified. The process may now require photographs and longer observations in the field to ensure the one species is not mistakenly perceived as two because at least two species of rain frogs can change their appearance.

Katherine Krynak believes the ability to change skin texture to reflect its surroundings may enable P. mutabilis to help camouflage itself from birds and other predators. The Krynaks originally spotted the small, spiny frog, nearly the width of a marble, sitting on a moss-covered leaf about a yard off the ground on a misty July night in 2009. The Krynaks had never seen this animal before, though Tim had surveyed animals on annual trips to Las Gralarias since 2001, and Katherine since 2005.

They captured the little frog and tucked it into a cup with a lid before resuming their nightly search for wildlife. They nicknamed it "punk rocker" because of the thorn-like spines covering its body. The next day, Katherine Krynak pulled the frog from the cup and set it on a smooth white sheet of plastic for Tim to photograph. It wasn't "punk "--it was smooth-skinned. They assumed that, much to her dismay, she must have picked up the wrong frog. "I then put the frog back in the cup and added some moss," she said. "The spines came back... we simply couldn't believe our eyes, our frog changed skin texture!

LEONARDO WILD's curator insight, April 1, 2015 9:28 AM

And they will find many more such oddities in Ecuador's many still mostly unexplored regions.

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Novel high-tech imaging method allows rapid imaging of vital functions in the living brain

Novel high-tech imaging method allows rapid imaging of vital functions in the living brain | Amazing Science |

Researchers studying cancer and other invasive diseases rely on high-resolution imaging to see tumors and other activity deep within the body's tissues. Using a new high-speed, high-resolution imaging method, Lihong Wang, PhD, and his team at Washington University in St. Louis were able to see blood flow, blood oxygenation, oxygen metabolism and other functions inside a living mouse brain at faster rates than ever before.

Using photoacoustic microscopy (PAM), a single-wavelength, pulse-width-based technique developed in his lab, Wang, the Gene K. Beare Professor of Biomedical Engineering in the School of Engineering & Applied Science, was able to take images of blood oxygenation 50 times faster than their previous results using fast-scanning PAM; 100 times faster than their acoustic-resolution system; and more than 500 times faster than phosphorescence-lifetime-based two-photon microscopy (TPM).

The results are published March 30 in Nature Methods advanced online publication ("High-speed label-free functional photoacoustic microscopy of mouse brain in action").

Other existing methods, including functional MRI (fMRI), TPM and wide-field optical microscopy, have provided information about the structure, blood oxygenation and flow dynamics of the mouse brain. However, those methods have speed and resolution limits, Wang says.

To make up for these limitations, Wang and his lab implemented fast-functional PAM, which allowed them to get high-resolution, high-speed images of a living mouse brain through an intact skull. This method achieved a lateral spatial resolution of five times finer than the lab's previous fast-scanning system; 25 times finer than its previous acoustic-resolution system; and more than 35 times finer than ultrasound-array-based photoacoustic computed tomography.

Most importantly, PAM allowed 3-D blood oxygenation imaging with capillary-level resolution at a one-dimensional imaging rate of 100 kHz, or 10 microseconds.

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Planets in the habitable zone around most existing stars, researchers calculate

Planets in the habitable zone around most existing stars, researchers calculate | Amazing Science |

Astronomers have discovered thousands of exoplanets in our galaxy, the Milky Way, using the Kepler satellite and many of them have multiple planets orbiting the host star. By analyzing these planetary systems, researchers from the Australian National University and the Niels Bohr Institute in Copenhagen have calculated the probability for the number of stars in the Milky Way that might have planets in the habitable zone. The calculations show that billions of the stars in the Milky Way will have one to three planets in the habitable zone, where there is the potential for liquid water and where life could exist. The results are published in the scientific journal, Monthly Notices of the Royal Astronomical Society.

Using NASA’s Kepler satellite, astronomers have found about 1,000 planets around stars in the Milky Way and they have also found about 3,000 other potential planets. Many of the stars have planetary systems with 2-6 planets, but the stars could very well have more planets than those observable with the Kepler satellite, which is best suited for finding large planets that orbit relatively close to their stars.

Planets that orbit close to their stars would be too scorching hot to have life, so to find out if such planetary systems might also have planets in the habitable zone with the potential for liquid water and life, a group of researchers from the Australian National University and the Niels Bohr Institute at the University of Copenhagen made calculations based on a new version of a 250-year-old method called the Titius-Bode law.

The law states that there is a certain ratio between the orbital periods of planets in a solar system. So the ratio between the orbital period of the first and second planet is the same as the ratio between the second and the third planet and so on. Therefore, if you knew how long it takes for some of the planets to orbit around the Sun/star, you can calculate how long it takes for the other planets to orbit and can thus calculate their position in the planetary system. You can also calculate if a planet is ‘missing’ in the sequence.

“We decided to use this method to calculate the potential planetary positions in 151 planetary systems, where the Kepler satellite had found between 3 and 6 planets. In 124 of the planetary systems, the Titius-Bode law fit with the position of the planets as good as or better than our own solar system. Using T-B’s law we tried to predict where there could be more planets further out in the planetary systems. But we only made calculations for planets where there is a good chance that you can see them with the Kepler satellite,” explains Steffen Kjær Jacobsen, PhD student in the research group Astrophysics and Planetary Science at the Niels Bohr Institute at the University of Copenhagen.

The researchers evaluated the number of planets in the habitable zone based on the extra planets that were added to the 151 planetary systems according to the Titius-Bode law. The result was 1-3 planets in the habitable zone for each planetary system. If you then take the calculations further out into space, it would mean that just in our galaxy, the Milky Way, there could be billions of stars with planets in the habitable zone, where there could be liquid water and where life could exist.

Corbin Baker's comment, May 3, 2015 5:10 PM
Astronomers have discovered thousands of exoplanets in our galaxy. Using the Kepler satellite and many of them have multiple planets orbiting the host star. A number of stars in the Milky Way that might have planets in the habitable zone. Where there is the potential for liquid water and where life could exist.
Corbin Baker's comment, May 3, 2015 5:29 PM
I think this is pretty cool. The possibility of there being water and life on other planets. What if that life is more advanced than us. What if there not friendly.
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Fecal transplants successful for treating C. difficile infection

Fecal transplants successful for treating C. difficile infection | Amazing Science |

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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Long-standing mystery in membrane traffic finally solved

Long-standing mystery in membrane traffic finally solved | Amazing Science |

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:

Risto Suoknuuti's curator insight, March 29, 2015 6:28 PM

Back to the roots.

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Could AI and Self-Flying Airplanes Have Prevented The Germanwings Crash?

Could AI and Self-Flying Airplanes Have Prevented The Germanwings Crash? | Amazing Science |

No level of security screening short of mind-reading could have prevented the crash of Germanwings flight 9525. But what can be done? The New York Times editorial calls for the American standard that requires two crew members be in the cockpit at all times to be adopted by “all airlines.” This suggestion is reasonable, but would not prevent a team of two pilots from accomplishing a similarly evil deed. The Times correctly asserts ”Air travel over all remains incredibly safe.”

The plane in question, the Airbus A320, has among the world’s best safety records and was the first commercial airliner to have an all-digital fly-by-wire control system. Much of the criticism over the years of these fly-by-wire systems has focused on the problem of pilots becoming too dependent on technology, but these systems could also be a means of preventing future tragedies. In fly-by-wire planes, a story on a previous Airbus crash in Popular Mechanics reports, “The vast majority of the time, the computer operates within what’s known as normal law, which means that the computer will not enact any control movements that would cause the plane to leave its flight envelope. The flight control computer under normal law will not allow an aircraft to stall, aviation experts say.” If autopilot is disconnected or reset, as the New York Times reports it was on the Germanwings plane, it can be switched to alternate law, “a regime with far fewer restrictions on what a pilot can do.”

AI pioneer Jeff Hawkins has addressed the recent upswell of fear about AI and “superintelligence” in a post on Re/code. “The Terminator Is Not Coming,” his title announces. “The Future Will Thank Us.” We are so concerned, it seems, about giving machines too much power that we appear to miss the fact that the largest existential threat to humans is other humans. Such seems to be the case with Germanwings 4U9525.

Hawkins is the inventor of the Palm Pilot (the first personal digital assistant or PDA) and the Palm Treo (one of the first smartphones). He is also the co-founder, with Donna Dubinsky, of the machine intelligence company NumentaGrok, the company’s first commercial product, sifts through massive amounts of server activity data on Amazon Web Services (AWS) to identify anomalous patterns of events. This same approach could easily be used to monitor flight data from airplanes and alert ground control in real time of the precise nature of unexpected activity. Numenta open sources its software ( and is known to DARPA and other government research agencies, so multiple parties could already be at work on such a system.

Hawkins’ approach to machine intelligence, Hierarchical Temporal Memory (HTM), has some distinct advantages over the highly-publicized technique of deep learning (DL). Both use hierarchies of matrices to learn patterns from large data sets. HTM takes its inspiration from biology and uses the layering of neurons in the brain as a model for its architecture. DL is primarily mathematical and projects the abstraction of the brain’s hierarchy to deeper and deeper levels. HTM uses larger matrices and flatter hierarchies to store patterns than DL and the data in these matrices is characterized by sparse distributions. Most important, HTM processes time-based data whereas DL trains mostly on static data sets.

For the emerging Internet of Things (IoT), time-based and real-time data is incredibly important. Systems that can learn continuously from these data streams, like Numenta’s, will be particularly valuable for keeping track of all of those things—including errant airplanes. Could machine intelligence have prevented this tragedy? Hawkins thinks so but notes, “All the intelligence in the world in the cockpit won’t solve any problem if the pilot decides to turn it off.” There will need to be aviation systems “designed for potential override from ground.” What are we the most scared of, individual agency or systematic control? Based on the Germanwings evidence so far,lack of override control from the ground is the greater threat.

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