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  • richardmitnick 10:27 am on June 22, 2017 Permalink | Reply
    Tags: Aneuploidy, , , COSMOS, Immune system response points way to beating cancer,   

    From COSMOS: “Immune system response points way to beating cancer” 

    Cosmos Magazine bloc


    22 June 2017
    Ariella Heffernan-Marks

    A scanning electron micrograph of a cancer cell in the process of dividing.
    Steve Gschmeissner / Getty

    After so many decades of searching for a cure for cancer, new research suggests a solution might have been within our own natural immune system the whole time.

    Angelika Amon, a biologist with the Massachusetts Institute of Technology in Boston, and colleague suggest exactly this in a study published in Developmental Cell. They report finding that cells with a high level of ‘chromosome mis-segregation’ – also known as ‘aneuploidy’ – elicit an innate immune response that results in their own cell-specific death.

    If this response could be replicated in cancer cells, the researchers say, it might provide a mechanism for their successful elimination.

    Aneuploidy occurs when chromosomes do not separate evenly during cellular division. This results in a chromosomal – and therefore genetic – imbalance in the cell. DNA damage, cellular stress, metabolic defect and alterations in gene dosage can also occur.

    Many diseases and disorders have consequently been associated with aneuploidy – including 70–90% of cancer tumours. It has been suggested that alterations in gene dosage can lead to changes in cancer-driver genes, resulting in the erratic proliferation patterns seen in cancer cells.

    Despite aneuploidy being confirmed as a hallmark of cancer, however, there is still debate over the exact link. Not all tumours show the same aneuploidy phenotype, and non-cancer sufferers with aneuploidy phenotypes, such as Down syndrome, tend to demonstrate lower chances of developing cancer, according to the Koch Institute for Integrative Cancer Research, with which Amon is also associated.

    Most normal tissues do not demonstrate aneuploidy. Even mutations in chromosome-alignment proteins do not result in high numbers of aneuploid cells, according to research published in Molecules and Cells.

    Thus the question is: what happens to the aneuploid cells?

    A popular explanation has been a “p53-activated mechanism”, whereby the complex karyotype (or chromosomal arrangement) of an aneuploid cell activates the protein p53, which stimulates mitotic arrest and cell death.

    Amon and her team, however, discovered this was not the case; rather, arrest and death was the result of an innate immune system response. Using live cell imaging and immunofluorescence, they observed chromosome mis-segregation through mutating chromosome alignment proteins and recorded the time to mitotic arrest. The p53 protein was activated regardless of chromosomes being mis-segregated.

    Amon and her colleague investigated the level of DNA damage due to aneuploidy by analysing protein gamma-H2AX, which is found only during double-strand DNA breaks. Elevated levels were found in aneuploid cells, indicating significant DNA stress and damage due to chromosome mis-segregation. Immunofluorescence confirmed this was generating complex karyotypes. “These cells are in a downward spiral where they start out with a little bit of genomic mess,” Amon explains, “and it just gets worse.”

    Additional gene analysis also indicated these cells had higher levels of innate immune cells compared to normal cells. Re-exposing both normal and aneuploid cells to these factors confirmed that specific factors were acting to selectively destroy aneuploid cells – most commonly the natural killer cell NK92. It is believed this could be in response to signals from DNA damage, cellular stress or irregularities in protein levels.

    So what does this mean with regards to finding the “cure to cancer”?

    Cancer cells have found a way to evade this cellular culling strategy. If researchers can find a way to re-activate this mechanism in aneuploid cancer cells, cancer treatment could use a NK92-mediated elimination method instead of toxic and expensive radioactive therapy.

    “We have really no understanding of how that works,” Amon concedes. “If we can figure this out, that probably has tremendous therapeutic implications, given the fact that virtually all cancers are aneuploid.”

    See the full article here .

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  • richardmitnick 11:56 am on June 20, 2017 Permalink | Reply
    Tags: , , , COSMOS, , Gene editing   

    From COSMOS: “Precision gene editing may deliver biofuel promise” 

    Cosmos Magazine bloc


    20 June 2017
    Elizabeth Finkel

    Biofuels from algae come with great promise. Santiago Urquijo/Getty Images

    For decades now, we’ve been promised cheap biofuels from algae. But there’s no free lunch. Growing these mini oil factories in vast ponds requires fertiliser and mechanical aeration; and then the oil has to be extracted. It all costs energy and money so the yields need to be high to make it worthwhile.

    One promising industrial species is Nannocholoropsis gaditana, which can produce a lipid – the oil and fat energy store – content up to about 60% of the algae’s ash-free dry weight. But Eric Moellering and colleagues at the company Synthetic Genomics Inc in California, wanted to do better.

    Starving the algae of nitrogen, paradoxically, boosts oil production. The problem is that the plants also curtail their growth so there’s no net gain. Ever since the 1970s, scientists have been trying to genetically engineer their way out of this quandary. But they’ve had to wait for the right tool: the bacterially derived CRISPR–Cas9 enzyme that has transformed ham-fisted genetic engineering into precision gene-editing.

    Moellering’s group identified a gene, called ZnCys, that was deactivated when the algae was starved of nitrogen. When the researchers completely disabled that gene, they saw oil production double, even without starving the algae.

    But the algae still grew poorly, so the scientists made use of the finesse of CRISPR–Cas9 to finely edit the DNA code of the ZnCys gene instead of disabling it competely. As they report in Nature Biotechnology this led to doubling oil yield without dampening algae growth.

    The final yield was up to five grams per square metre of algae per day.

    Amazing what a good editor can do!

    See the full article here .

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  • richardmitnick 10:46 am on June 19, 2017 Permalink | Reply
    Tags: , COSMOS, Homeostatic equilibria, Niles Eldredge, Palaeontology, Stephen Jay Gould, Theory of Evolution, Theory of punctuated equilibria   

    From COSMOS: “New model backs controversial idea of how evolution works” 

    Cosmos Magazine bloc


    19 June 2017
    Andrew Masterson

    American Palaeontologist Stephen Gould. Wally McNamee/CORBIS/Corbis via Getty Images

    In 1972 the eminent palaeontologist Stephen Jay Gould and his colleague Niles Eldredge proposed an idea about the way evolution worked and, in so doing, sparked a fight of almighty proportions.

    New modelling revealed by Michael Landis and Joshua Schraiber of Temple University in Pennsylvania, US, however, adds considerable extra weight to their case.

    Gould and Eldredge sought to explain so-called gaps in the palaeontological record – missing fossils assumed to represent transitional phases between ancient species and the modern ones into which they evolved – by suggesting they were an illusion.

    Evolution, they proposed, wasn’t a gradual process, marked by the slow accumulation of new characteristics. Rather, they said, “the history of evolution is not one of stately unfolding, but a story of homeostatic equilibria, disturbed only ‘rarely’ … by rapid and episodic events of speciation.”

    Two important principles underpinned their explanation, which they dubbed the theory of punctuated equilibria.

    The first was that once a species evolved, it tended to stay pretty much the same from thereon in until extinction ended its run. The second was that when part of a species became isolated from the rest and thus fell under new selection pressure, if it was going to evolve into something new it would do so very quickly (at least, on a geological scale).

    “If new species arise very rapidly in small, peripherally isolated local populations,” the pair wrote, “then the great expectation of insensibly graded fossil sequences is a chimera.”

    The theory was roundly attacked by some other prominent voices in the field. In his book, The Blind Watchmaker, Richard Dawkins said punctuated equilibrium was an idea that “does not deserve a particularly large measure of publicity”.

    Philosopher Daniel Dennett, in his book Darwin’s Dangerous Idea, also slammed Gould – who responded by calling him “Dawkins’ lapdog”. Dennett shot back that in doing so Gould was “turn[ing] up the volume of his vituperation.”

    Gould died in 2004, Dennett is now 75, and the debate is still a long way from settled.

    However, Landis and Schraiber, publishing on the preprint site bioRxiv, push the argument back in favour of speciation as a comparatively rapid, rather than gradual, process.

    The title of their paper serves also as its bold conclusion: Punctuated evolution shaped modern vertebrate diversity.

    The pair constructed a mathematical model based on random probability distribution and fed in datasets derived from the morphological characteristics of about 50 clades (genetically-related groups of animals) covering mammals, birds, reptiles, fish and amphibians.

    The results fitted best within a framework of punctuated development, with long periods of stasis – averaging around 10 million years – between “jump processes” of “pulsed evolution” lasting as little as 100 generations.

    All of the data used concerned modern species. Landis and Schraiber suggest that future work integrating their work with the paleontological evolutionary research kick-started by Gould and Eldredge will throw up more detailed evidence about how rapid spurts of evolution and speciation are related.

    The reactions of professors Dawkins and Dennett remain unknown, but might be memorable.

    See the full article here .

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  • richardmitnick 8:07 am on June 15, 2017 Permalink | Reply
    Tags: , Broccoli, COSMOS, , Sulforaphane,   

    From COSMOS: “Broccoli may hold key to new diabetes treatment” 

    Cosmos Magazine bloc


    15 June 2017
    Andrew Masterson

    Sulforaphane, a compound found in broccoli, may help in the treatment of type 2 diabetes. Bernard Jaubert

    A chemical compound found in broccoli offers a potential treatment alternative for type 2 diabetes, a study in Science Translational Medicine reveals.

    The compound, sulforaphane, emerged as a possible drug-development target after a team led by Annika Axelsson, of the Lund University Diabetes Centre in Malmö, Sweden, constructed a “disease signature” for type 2 diabetes based on 50 genes and compared the result to “drug signatures” that map interactions between chemicals and their genetic targets.

    Axelsson’s team tested 3,852 compounds and found that sulforaphane – present in many cruciferous vegetables, but especially in broccoli – seemed especially promising.

    In the laboratory the team found that the compound reduced glucose production in cultured human liver cells, and altered liver gene expression in diabetes-affected rats.

    In a follow up trial, Axelsson and colleagues enrolled 97 patients with type 2 diabetes and conducted a 12 week trial, with cohorts given daily concentrated broccoli extract or a placebo control.

    They discovered that the extract “exerts a sustained effect on gene expression”. Obese patients receiving the extract showed significant improvement, they report.

    Sulforaphane has been the focus of much previous research, particularly because of its observed cancer-protective effects, which it achieves by improving the body’s anti-oxidation ability. A March 2017 Japanese study also found it can be used to control obesity. [ https://www.sciencedaily.com/releases/2017/03/170307100402.htm ]

    The compound’s use in managing type 2 diabetes could be of particular appeal for the estimated 15% of patients who cannot take the standard treatment, metformin, because in some cases it can increase the risk of kidney damage.

    However, the scientists caution that the results so far, while encouraging, are still preliminary. Sulforaphane’s clinical deployment, they write, “cannot yet be recommended to patients as a drug treatment but would require further studies, including data on which groups of patients would potentially benefit most from it”.

    See the full article here .

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  • richardmitnick 4:37 am on June 14, 2017 Permalink | Reply
    Tags: , , COSMOS,   

    From COSMOS: “How dissolving cells reveals cancer secrets’ 

    Cosmos Magazine bloc


    13 June 2017
    Anthea Batsakis

    A decellularised mouse mammary gland, stained to show collagen IV, an important molecule in the extracellular matrix. Thomas Cox

    The microscopic structure of tumours has always remained somewhat elusive for biologists. But thanks to a new technique, scientists have, for the first time, seen in three dimensions the “net” that holds our cells in place and gives tissues their shape, known as the extracellular matrix.

    Led by Janine Erler from the University of Copenhagen, where the research took place, this technique may help reveal the architecture of tumours and explain why tumours can grow back in different parts of the body after being removed.

    Until now, studying the extracellular matrix required tissue to be sliced into tiny strips and dropped into a beaker of solution – at best, this technique showed the matrix in two dimensions.

    In research published in Nature Medicine, the scientists instead used blood vessels to transport cell-removing compounds into mouse organ tissue, gently dissolving the cells and hollowing out the organ to leave behind its delicate scaffolding. They call the technique in situ decellurisation of tissue, or ISDoT.

    The fibres of the extracellular matrix, made up of a complex lattice of proteins and carbohydrates secreted from cells, can be seen with far greater clarity without the cells obstructing the view.

    Thomas Cox, one of the authors of the paper, is a cancer cell biologist from the Garvan Institute in Sydney, Australia. “We’ve seen things that we never would have expected and we don’t know exactly what they mean, but that’s all part of the fun,” he says.

    “No has ever seen this before and we’ve got plenty to keep us busy to follow up on.”

    As well as giving physical structure to our tissues, the extracellular matrix also has a powerful influence on cell behaviour.

    When it comes to tumours, the extracellular matrix and cancer cells manipulate one another. Cancer cells, for instance, can create more of the matrix, destroy it and remodel it.

    “This is why our study is important, because it has been shown that as cancer cells change their environment, they’re more able to go on and multiply uncontrollably,” Cox says.

    Using mass spectrometry, Cox and his colleagues identified and catalogued different components of the matrix. Interestingly, they found that the way secondary cancer cells (metastases) remodel the matrix is specific to the organ they’re growing within.

    Queensland University of Technology breast cancer biologist Rik Thompson, who didn’t take part in the study, says the varying structure of the matrix in secondary tumours might be why they’re more difficult to treat.

    “This is exciting in that it provides a robust, validated approach for examining extracellular matrix and already has shown some very new information,” Thompson says.

    “The mass spectroscopy takes the study to a new dimension, with hundreds of proteins identified to vary in the extracellular matrix around cancers compared to the normal tissues.”

    He adds that this new technique will influence his own research on how proportions of breast tissue plays into the risk of breast cancer.

    “This approach would enable us to more comprehensively understand the structure and composition of the extracellular matrix in regions of high versus low mammographic density.”

    See the full article here .

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  • richardmitnick 8:26 am on June 7, 2017 Permalink | Reply
    Tags: Abell 115, , , , , COSMOS, Space hots up when galaxy clusters collide   

    From COSMOS: “Space hots up when galaxy clusters collide” 

    Cosmos Magazine bloc


    07 June 2017
    Andrew Masterson

    Galaxy clusters like the one shown above are fascinating astrophysical laboratories.
    NASA, ESA, and B. Siana and A. Alavi (University of California, Riverside)

    NASA/ESA Hubble Telescope

    What do you get when a pair of galaxy clusters, both moving at very high speeds speeds, slam into each other?

    A whole lot of heat, it turns out, in a finding that has surprised observers.

    Astronomers from the University of Colorado at Boulder have been watching two enormous galaxy clusters that are merging to create an even bigger cluster dubbed Abell 115, some 2.4 billion light years away.

    In an unexpected outcome, the collision between the two clusters has produced a turbulent region of hot gas, with temperatures reaching 1.7 million degrees Celsius. That’s approximately three times hotter than either of the cluster cores.

    Study leader Jack Burns likens the phenomenon to the wake produced by a fast moving motor-boat.

    “We did not expect to see such very hot gas between the cluster components,” he says.

    “We think the turbulence is like a big spoon stirring up gases, converting the energy of motion from the merging clusters into thermal energy. It is a manifestation of them banging together like two giant pots, something we have not really seen before.”

    To estimate the temperature of Abell 115, Burns and his team developed software to create high contrast temperature maps of all the regions in the two colliding clusters, using the X-ray and radio portions of the electromagnetic spectrum.

    The results were then fed through NASA’s Ames Research Centre supercomputer.

    As well as the unexpected heat produced, the results also show that the newly forming super-cluster is sending radio emissions a long way out into deep space.

    “These radio emissions are caused by electrons in the magnetic field of the galaxy cluster traveling at near the speed of light,” says Burns.

    “Clearly something has energised the electrons, which we think is related to the cluster banging process.”

    Each of the clusters contains hundreds of galaxies, many the size of the Milky Way. Their collision, says Burns, is one of the “biggest bangs in the universe since the Big Bang”.

    The team predicts that eventually the turbulence created by the collision will abate and the new mega-cluster will reach some form of equilibrium.

    “We believe Abell 115 will eventually ‘relax’ and become centrally condensed,” says Burns, “which is relatively boring compared to what we are seeing now.”

    The findings were presented this week to the 230th Meeting of the American Astronomical Society, held in Austin, Texas.

    See the full article here .

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  • richardmitnick 8:14 am on June 7, 2017 Permalink | Reply
    Tags: , COSMOS, , Hidden landscapes of the deep sea floor, Visual Soundings   

    From COSMOS: “Hidden landscapes of the deep sea floor” 

    Cosmos Magazine bloc


    07 June 2017
    Sarah Condie

    Scientific imaging captured lava flowing from a recent submarine volcanic eruption, taking the form of a brain in its complexity and shape. Visual Soundings

    Human kind has explored the surface of the moon, documenting craters and studying rock formations. Thanks to NASA’s rovers, we’ve even gone as far as Mars, familiarising ourselves with the appearance of the dusty red planet. But, only five percent of the world’s oceans have been mapped in any detail. There’s a whole world beneath us, supporting human life, that remains a mystery.

    In recent years, however, significant inroads have been made to uncover the elusive and gargantuan world lying underneath the waves. New acoustic images released by Visual Soundings have given us a unique insight into deep sea landscapes.

    Technological advances in scientific imaging can now use sound and vibration to illuminate the seafloor, revealing stunning patterns and images rarely seen by human kind. Usually studied with a scientific eye, the beauty and wonder of marine landscapes are often overlooked.

    Co-founder of the initiative, IMAS scientist Dr Vanessa Lucieer, shares that “new techniques such as multibeam echosounders have revolutionized scientists’ knowledge of the appearance, shape and structure of the seabed.

    In doing so, they sometimes reveal startlingly beautiful glimpses of the seafloor that look more like works of art than scientific data.”

    In partnership with her colleague and fellow marine scientist Dr Margaret Dolan, Dr Lucieer hopes that these images will promote the wonder of the ocean, encouraging people to take responsibility and action in its ever-important conservation.

    You can discover more incredible images and find out how they were captured on the Visual Soundings website.

    See the full article here .

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  • richardmitnick 11:31 am on May 29, 2017 Permalink | Reply
    Tags: , COSMOS, Doped diamond, , , Superposition   

    From COSMOS: “Doped diamond may lead to everyday quantum computers” 

    Cosmos Magazine bloc


    29 May 2017
    Andrew Masterson

    Precise placement of atoms in a diamond lattice may be a handy technique for quantum computer manufacture. Victor Habbick Visions / Getty

    Quantum computers are still halfway mythical, but they are moving closer to reality step by tiny step.

    One of the most widely favoured structures for building viable quantum computers is a diamond surface dotted with irregularities only a couple of atoms wide.

    The problem researchers face, however, is making sure those irregularities – essentially atom-scale holes and accompanying bits of atom-wide foreign material – are drilled into the diamond substrate in exactly the right spot.

    A report at Nature Communications by a team from MIT, Harvard University, and Sandia National Laboratories, in the US, covers a new method of doing so, creating the “defects” in the diamond crystal structure within 50 nanometres of their optimal locations.

    The precise placement of the irregularities – known as “dopant-vacancies” in the business – is a critical outcome if quantum computers are ever to end up on the market.

    This is because the combination of a tiny hole and a couple of atoms of non-diamond matter – nitrogen, for instance – can be engineered to act as a qubit, the fundamental element of quantum computing.

    At the heart of a qubit is a subatomic particle that can simultaneously occupy a number of contradictory states – on, off, and a “superposition” of both together, for instance. The combination of the hole, the foreign atoms, and the light refracted through the diamond combine to create an elegant qubit.

    At least, theoretically. To date, most experimental work has been done using nitrogen dopant-vacancies. These have the advantage of being able to maintain superposition longer than other candidates, but emit light across a broad range of frequencies, making information retrieval difficult.

    The MIT-Harvard-Sandia team, led by Tim Schröder, experimented instead with silicon-based defects, which emit light in a much narrower range. That advantage, however, comes with its own challenge: the silicon dopant-vacancies need to be chilled to within a few thousands of a degree above absolute zero if they are to maintain a superposition for any length of time.

    That remains a challenge still to be met, however. The import of the current study, published in the journal Nature Communications, lies in the increase in the accuracy of positioning the defects in the diamond.

    To achieve this, scientists at MIT and Harvard first created a sliver of diamond only 200 nanometres thick. Onto this they etched tiny cavities.

    The substrate was then sent to the Sandia laboratories, where each cavity was bombarded with 20 to 30 silicon ions. The process led to only about two percent of the cavities attracting silicon residents.

    Back at MIT a second new process was employed. The diamond sliver was heated to 1000 ºC, at which temperature its component lattice became malleable, allowing the researchers to align more cavities with more silicon particles – taking the total number of dopant-vacancies to 20%.

    Most of the irregularities thus produced were within 50 nanometres of their optimal position, and shone at around 85% of optimal brightness.

    A quantum computer in every household is still a long way off, but this study marks a potentially important step in the journey.

    See the full article here .

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  • richardmitnick 11:15 am on May 29, 2017 Permalink | Reply
    Tags: A bubble around Earth, , , , , COSMOS,   

    From COSMOS: “Radio signals may have created a protective magnetic bubble around Earth” 

    Cosmos Magazine bloc


    29 May 2017
    No writer credit found.

    Very low frequency radio communications with deep-sea submarines may keep out high energy electrons and protons.


    Very low frequency (VLF) radio communications – the kind we use to communicate with submarines, far below sea level – could be creating a bubble around Earth that protects against high levels of space radiation.

    NASA’s Van Allen Probes have observed the extent to which excess space radiation, in the form of highly-charged particles, moves into our near-Earth environment.

    Van Allen Belts NASA GSFC

    NASA Van Allen Probes

    A new paper at SpringerLink from researchers at the University of Colorado’s Laboratory for Atmospheric and Space Physics in Boulder, US, observes that the outer limit of the bubble of radio waves around the planet caused by VLF communication is about the same as the inner limit of the Van Allen radiation belts – layers of charged particles held in place by Earth’s magnetic fields.

    The paper suggests that this may not be a coincidence – that perhaps our radio waves are impacting how particles move in space. Indeed, in the 1970s, before VLF communication was in widespread use, it appears radiation was present further into our near-Earth atmosphere.

    If this analysis is accurate, VLF transmission could be used to remove excess radiation from the Earth’s atmosphere. Further research is underway to test the impact of VLF transmissions on charged particles in our upper atmosphere.

    See the full article here .

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  • richardmitnick 3:09 pm on May 26, 2017 Permalink | Reply
    Tags: , , , , COSMOS,   

    From COSMOS: “CubeSats: exploring other planets on a budget” 

    Cosmos Magazine bloc


    26 May 2017
    Cathal O’Connell

    Anthony Calvert
    Hitchhiking could be the new way to see the solar system. No towel required.
    Name: Mars Cube One (MarCO)
    Destination: Martian orbit
    Mission cost:
    (MarCO) US$13 million,
    (Insight) US$425 million
    Launch Date: 20 May 2018
    Mars Arrival: 26 November 2018
    Dimensions (while stowed): 36.6 x 24.3 x 4.6 x 11.8 cm.
    Mass: 14 kg

    Any man who can hitch the length and breadth of the galaxy, rough it, slum it, struggle against terrible odds, win through, and still knows where his towel is is clearly a man to be reckoned with.” – Douglas Adams

    Exploring the solar system is absurdly expensive. Even a single mission, such as NASA’s US$675 million InSight probe to Mars, scheduled to launch in May 2018, would eclipse the total science budget of most nations.

    NASA Mars Insight Lander

    But with tiny, hitchhiking satellites called CubeSats, there may finally be a way to explore other planets on a shoestring.

    Tagging along on that InSight mission will be two CubeSats – small, boxy satellites the size of a carry-on suitcase. Built by NASA’s Jet Propulsion Laboratory, these Mars Cube One (or MarCO) probes will be the first CubeSats to voyage to another planet. If they pull off their US$13 million mission – peanuts compared with any previous interplanetary mission – MarCO could lead to a shift in how we explore the solar system, even opening the doors to smaller nations to stake a claim. Space travel finally has an economy-class fare.

    CubeSats were originally designed as a training tool, so university students could design and build satellites in the timeline of a semester. The basic idea was to cram the instrumentation into a standard template: a cube with 10 cm sides.

    Almost 20 years on, more than 500 cubesats have been launched successfully into orbit, with another 600 launches planned for 2017 alone. CubeSats have turned into the great leveller of modern space exploration, achievable within the budget of schools, universities, or even crowdfunding campaigns.

    See the full article here .

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