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CRISPR: the next generation of genome editing tools

CRISPR: the next generation of genome editing tools | Science Garden | Scoop.it

An arms race has been waged between bacteria and bacteriophage that would bring a satisfactory tear to Sun Tzu’s eye. Scientists have recently recognized that countermeasures developed by bacteria (and archaea) in response to phage infections can be retooled for use within molecular biology. In 2013, large strides have been made to co-opt this system (specifically and most commonly from Streptococcus pyogenes) for use in mammalian cells. This countermeasure, CRISPR (clustered regularly interspaced short palindromic repeats), has brought about another successive wave of genome engineering initiated by recombineering and followed more recently by zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs).

 

ZFNs and TALENs perform a similar function yet the learning curve appears to be more difficult for development due to the use of protein-DNA contacts rather than the simplicity of designing RNA-DNA homology contacts. Although the potential for CRISPR in regards to genome editing within mammalian cells will be of greatest interest to the reader, the CRISPR backstory is equally compelling. Just as we have evolved immune responses to pathogens, so too have bacteria. CRISPR is an adapted immune response evolved by bacteria to create an immunological memory to ward off future phage infections. When a phage infects and injects its DNA within a bacterium, the DNA commandeers bacterial proteins and enzymes for use towards lytic or lysogenic phases. However, exposure of phage DNA allows the bacterium to copy and insert snippets (called spacers) of phage DNA into its genomic DNA between direct repeats (DR). These snippets can later be expressed as an operon (pre-CRISPR RNA, pre-crRNA) alongside a trans-activating CRISPR RNA (tracrRNA) and an effector CRISPR associated nuclease (Cas). Together these components surveil for foreign crRNA cognate sequence and cleave the targeted sequence.

 

Although hallmarks of CRISPR have been known since the late 80’s (CRISPR timeline) and was acronymed in 2002, Jinek et al. in August 2012 were the first to suggest the suitability of CRISPR towards genome editing. In February of 2013, Feng Zhang’s and George Church’s labs simultaneously published the first papers describing the use long oligos/constructs for editing via CRISPR in mammalian cells and made their plasmids readily available on Addgene. Zhang’s lab went one step further and has supplemented their papers with a helpful website and user forum. They have even gone so far as to publish a methods paper to streamline the use of their plasmids towards a plug-and-play, modular cloning approach with your target sequence of interest.

 

CRISPR works fairly well out of the box yet still has some imperfections that are being addressed. For example, CRISPR relies upon a protospacer adjacent motif (PAM; S. pyogenes sequence: NGG) 3’ to the targeting sequence to permit digestion. Although the ubiquity of NGG within the genome may seem advantageous, it may be limiting in some regions. Other species make use of different PAM sites that can be considered when choosing a cut sites of interest. Since double-stranded cuts could potentially create DNA lesions (a byproduct of the cell using non-homologous end joining [NHEJ] instead of homologous recombination) some labs are choosing to use modified Cas enzymes that nick DNA, instead of creating a double-strand break. This potential weakness of CRISPR to create DNA lesions via NHEJ, however, has been exploited by Eric Lander’s and Zhang’s lab this month (Jan. 2014). They have capitalized on the cell’s use of NHEJ to manufacture DNA lesions (frameshift mutations) at cut sites within genes on a large scale as a means to perform large genetic screens. Using this technique knocks out a gene and has the obvious advantage of fully ablating a gene’s expression compared to RNAi where some residual expression can be expected.

 

The advantages of CRISPR lends itself to future therapies. High efficiency, low-to-no background mutagenesis and easy construction put CRISPR front and center as the tool de jour for gene therapy. In combination with induced pluripotent stem cells (iPSCs), one can imagine the creation of patient-specific iPSCs created with non-integrative iPSC vectors and modified by CRISPR, devoid of any residual DNA footprint left behind by the iPSC vector or CRISPR correction. In conjunction with whole genome sequencing, genetically clean cell lines can be selected that are suitable for differentiation towards the germ layer of interest for subsequent autologous transplantation. Proof of principle experiments have already been published in models of cystic fibrosis and cataracts.

 

For better or worse, CRISPR is catching on like wildfire with young investigators, as noted recently by Michael Eisen. What may be looming in the future and not as openly discussed at this time is the potential for CRISPR to open up the genome to large scale editing. We tend to think of any particular genome as fairly static with slight variations between any two individuals and increased variation down the evolutionary line. However, CRISPR has proven to be a fantastic multitasker, capable of modifying multiple loci in one fell swoop as demonstrated by the Jaenisch lab (five loci). With the creation of Caribou Biosciences and a surprising round of venture capital raised by a powerhouse team at Editas Medicine in November ($43 million), CRISPR appears to also have sparked an interest in the private sector. With large sums of money at their disposal, these companies can now begin to look at the genome, not as a static entity, but more akin to operating system, a code that now has a facile editing tool. George Church, an Editas co-founder, has speculated in the past about the potential use of the human genome as the backbone for recreating the Neanderthal genome in his recent book and interview with "Der Spiegel". In an era where the J. Craig Venter Institute can create an organism’s genome de novo and a collaboration between Synthetic Genomics and Integrated DNA Technologies has proposed to synthesize DNA upwards of 2Mbp, the combination of CRISPR, synthetic DNA and some elbow grease will make the genome more accessible and Church’s speculations a potential reality.


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It's David Bowie Day In Chicago

It's David Bowie Day In Chicago | Science Garden | Scoop.it
Last week, Chicago Mayor Rahm Emanuel declared September 23rd (today) David Bowie Day in honor of the city's connection with David Bowie Is, a career
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Engineered proteins from mussles and barnacles stick like glue—even in water

Engineered proteins from mussles and barnacles stick like glue—even in water | Science Garden | Scoop.it
Shellfish such as mussels and barnacles secrete very sticky proteins that help them cling to rocks or ship hulls, even underwater. Inspired by these natural adhesives, a team of MIT engineers has designed new materials that could be used to repair ships or help heal wounds and surgical incisions.

 

To create their new waterproof adhesives, the MIT researchers engineered bacteria to produce a hybrid material that incorporates naturally sticky mussel proteins as well as a bacterial protein found in biofilms—slimy layers formed by bacteria growing on a surface. When combined, these proteins form even stronger underwater adhesives than those secreted by mussels.

 

This project, described in the Sept. 21, 2014 issue of the journal Nature Nanotechnology, represents a new type of approach that can be exploited to synthesize biological materials with multiple components, using bacteria as tiny factories.

 

"The ultimate goal for us is to set up a platform where we can start building materials that combine multiple different functional domains together and to see if that gives us better materials performance," says Timothy Lu, an associate professor of biological engineering and electrical engineering and computer science (EECS) and the senior author of the paper.

 

The researchers tested the adhesives using atomic force microscopy, a technique that probes the surface of a sample with a tiny tip. They found that the adhesives bound strongly to tips made of three different materials—silica, gold, and polystyrene. Adhesives assembled from equal amounts of mussel foot protein 3 and mussel foot protein 5 formed stronger adhesives than those with a different ratio, or only one of the two proteins on their own.

 

These adhesives were also stronger than naturally occurring mussel adhesives, and they are the strongest biologically inspired, protein-based underwater adhesives reported to date, the researchers say. The team also plans to try to create "living glues" consisting of films of bacteria that could sense damage to a surface and then repair it by secreting an adhesive.


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Goats, chickens, bees, & weeds. That's an Urban Ag wrap

What happens when you introduce urban students of all ages and backgrounds to the world of local Chicago urban farming? Beautiful and very cool things. 

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Get Ready For The Autumnal Equinox! - Farmers' Almanac

Get Ready For The Autumnal Equinox! - Farmers' Almanac | Science Garden | Scoop.it

Monday, September 22, at 10:29 p.m. (EDT) is the Autumnal Equinox for 2014. This is the moment when the Sun crosses the Equator and those of us living in the Northern Hemisphere begin to see more darkness than daylight. Regardless of whether it has been chilly for weeks or there are still balmy summer-like temperatures, this day is the official start of autumn.

 

So what does that mean? Essentially, our hours of daylight — the period of time each day between sunrise and sunset — have been growing slightly shorter each day since the Summer Solstice in June, which is the longest day of the year (at least in terms of light). Even after three months of shortening days, though, we still see more light than darkness over the course of a day.

 

The Autumnal Equinox marks the turning point, when darkness begins to win out over daylight. For the next three months, our hours of daylight will continue to grow shorter. At this equinox, day and night are approximately equal in length. The name ‘equinox’ comes from the Latin word aequus, meaning equal, and nox, meaning night.  An equinox occurs twice a year (Autumnal and Vernal).

 

Everywhere you look, you can see the visible changes as nature prepares for winter: birds are flying south, temperatures are getting cooler, leaves are changing colors, and animals’ coats are thickening, to name a few.


In December (on December 21, 2014, at 6:03 p.m. EST, to be exact) we will experience the Winter Solstice, the shortest day of the year in terms of hours of daylight.

 

After the Winter Solstice, the days will begin to grow longer again. It will take another three months, until the Vernal Equinox (March 20, 2015, at 6:45 p.m. EDT) for the periods of daylight and darkness to reach equilibrium once again.

 

From the Vernal Equinox, the days will continue to grow longer, until we reach the Summer Solstice again on June 21, 2015, at 12:38 p.m. EDT., and the whole cycle begins anew!

 

Here are the official dates for each of the seasons for 2014 and 2015.

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Keeping dogs out of flower beds

Keeping dogs out of flower beds | Science Garden | Scoop.it

Save your pine cones for bedding, which will keep pups and cats out of your plants.


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Ivan Logvenoff's curator insight, May 15, 1:50 AM

Une idée pour éloigner les animaux des plantations récentes en milieu urbain. A tester plutôt sur des massifs de plantes acidophiles.

Sharilee Swaity's curator insight, May 17, 10:08 AM
Cats do love plants, but you don't want them ruining your hard work. Some ways to detract them from digging up the gardens or flowers.
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What can you do when your neighbor's herbicide burns down your organic crops?

What can you do when your neighbor's herbicide burns down your organic crops? | Science Garden | Scoop.it

By Mike Sula

At first, when Stephanie Douglass saw the orange spots covering plants and trees all over the ten-acre organic farm she manages, she thought it might be some sort of fungus or bacterial infection. The spotting on the leaves was indiscriminate, attacking everything from tomatoes to peppers to cucumbers to basil to sunchokes to spinach. Within two weeks the tissue on some of most heavily affected plants necrotized and developed holes, giving their leaves the texture of Swiss cheese. Douglass figured at least 85 percent of the crops were affected.

"If this is a fungus or bacteria," she told herself, "then we are ground zero for something that can spread in one-and-a-half days and jump crop families. That's very bad."

 

Douglass is the manager of the Les Brown Memorial Farm, in downstate Marseilles, a little under an hour and a half southwest of the two urban farms her employer operates in Englewood and Back of the Yards. Set on a decommissioned weather station, the plot has been farmed by Growing Home with the blessing of the federal government since 2002, under the condition that the organization serve the homeless in some way, which it does by offering job training and work experience to its employees, or "production assistants," many of whom have been homeless or incarcerated. The farm operates an on-site farm stand and a CSA program for around 100 customers, and also sells produce at the Green City and Logan Square farmers' markets. Running along lonely North 30th Road, it's surrounded on all sides by fields that rotate genetically modified soybeans and corn. This season it's soybeans as far as the eye can see.

 

Douglass and her assistant took to the Internet to investigate what had assailed their crops, but not finding anything natural that looked like what they were seeing, they began to suspect pesticide. They found plenty of photos of plants destroyed by chemical herbicides that looked a lot like what they were seeing in the fields.

And that made sense given what they'd observed earlier in their neighbors' fields. Douglass says the previous Monday—Memorial Day—she noticed someone with a mobile pesticide applicator spraying in the fields to the north and west of the property. That Tuesday she was in the city, but her assistant says she saw someone in the field to the south spraying with a much larger rig. That's not unusual, unless it's a windy day. And it was windy.

 

The day after Douglass discovered the damage, she filed a pesticide misuse complaint with the Illinois Department of Agriculture's Bureau of Environmental Programs, who would send out an inspector to determine whether there had been any violations of the Illinois Pesticide Act, in particular, the "use of a pesticide inconsistent with the labeling of the pesticide," in the vernacular of the BEP. Douglass also called the Midwest Organic Services Association, the certifying organization that makes sure Growing Home and around 1,500 other farms and produce handlers are operating within the guidelines set by the USDA's National Organic Program. Naturally, those include strict prohibitions on the use of chemical fertilizers, pesticides, and herbicides.

 

This particular call had the potential to lead to serious consequences for the farm. Beginning last year, the federal government began to require certifying agencies to test for pesticide residue among 5 percent of the operations they certify. MOSA would send an inspector to Marseilles to collect samples of damaged plants, which would be sent to a lab in Minnesota for testing. If the results showed the presence of any of more than 185 prohibited chemicals—from acephate to vinclozolin—the farm could be held in violation, prohibited from marketing its produce as organic and forced back into the three-year probationary transition period all farms must pass in order to be certified organic.

 

Normally certifying agencies identify the farms to be tested, but occasionally a farm will report the problem voluntarily, and Douglass is committed to the system. "In my opinion, according to their standards, if any form of herbicide or pesticide appeared in the fields, we are in violation," she says. "I'm kind of a stickler, and I believe in what organic means. And so I was telling them from the beginning, 'Let me know. So I can let my customers know.'"

 

In the meantime, Douglass says, MOSA told her she should proceed with her work. She could transplant the damaged seedlings in the hoop houses to the fields and carry on as normal. And she could continue to sell her produce as organic. But Douglass wanted her customers to know something had happened. In her weekly CSA newsletter she informed them of the leaf spotting and of her efforts to get to the bottom of it, and reported that officials had told her the produce was safe to eat. "The silver lining is," she wrote, "whoa are you guys getting a real, firsthand look at what it's like to run a small organic farm in Big Ag country!"

 

The state inspector arrived a week later. Douglass says he voiced skepticism that the farm had suffered any pesticide spray drift: most of the incidents he was called out for turn out to be petty disputes between neighbors. "He said, 'We're probably not going to need to do any tests.' And then as soon as he saw it, he starts walking to his car. I'm like, 'What are you doing?' He's like, 'I'm going to get my testing kit.'" The inspector took plant samples and left, and Douglass continued to wait.

 

To read the rest of the article: http://www.chicagoreader.com/chicago/farming-pesticide-drift-growing-home-driftwatch-hintzsche/Content?oid=15017654

 

 

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Giant DNA Origami

Giant DNA Origami | Science Garden | Scoop.it

Researchers create the largest 3-D DNA structures to date, many times bigger than previously constructed origami shapes.


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Meet Strati, the first 3D printed car in the world

Meet Strati, the first 3D printed car in the world | Science Garden | Scoop.it
While some people have successfully 3D printed buildings, others have taken the same approach to the car manufacturing business, as a company has just come out with a car called the Strati that's t...

Via Tiaan Jonker
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Mohmed Ali's curator insight, September 22, 12:20 AM

SOLUTIONS FOR SOCIAL JUSTICE AND COMMON GOOD ALLOVER THE WORLD.

 Kind attention to all Jewish,Christians,Muslims and all other communities in the world Holy Quran is containing of 6666 verses which are dedicated  to angles by God. Out of it 87% of verses are related to Histories of Prophets and Wars , Earthquakes, Floods and Famine which affected the people who were residing at the time of Prophets . Muslims in the world are reciting whole Quran verses  frequently in all the Muslim countries and countries wherein muslims  are residing . they are affecting by  wars , Disasters , Tsunami , Earthquakes , Climate changes , loss of business , terrorism and also creating other problems with other communities  on the reasons that 6666 Quranic verses are handled  by angles in the world in accordance with Quranic Verses 42:51,52 According to Quranic verses 39:17, 18  and 55 , It is revealed  that  whole quran verses cannot be recited except very important verses can be recited towards social justice and common good for the purpose of peace , unity , health , wealth , faith , inter-faith , climate changes , improving business and stopping off disasters and terrorism and accordingly we have posted messages of God and also our research paper at www.goldenduas.com for the same purpose in accordance with all the international laws as follows:   Nowdays, all the governments in the world or collecting huge taxes from tax payers and the same are utilizing for the purpose of peace in the world, but no result. The tax payers are suffering to improve their business and life. The following points may be taken in account to solve all the world challenges and disbute.Proposal to the United Nations relating to International Peace and Security to authorize Under Article 96(2) of the Charter of the United Nations. Hello,Our research report  is in conformity with Under Article 1(1) and 7 of the Charter of United Nations and the same maybe authorized by the General Assembly of the United Nations  in accordance with U/A 96(2) of the present Charter and U/A 2(2), 5(1),6(2),11(2),13(1), 15(1) (a) (c), 16(2) (a),(b),& 18 of the International Covenant on Economic, Social and Cultural Rights on the basis of U/A 33(1), 55(c), 70, 71,73(a) of the present Charter and accordingly  the research paper ought to have been debated with Vatican, World Churches Council, Commission of Churches on International Affairs, Jewish Foundation, Islamic Supreme Councils , researchers of UN and all the International bodies for the following reasons:“Reporting of world peace solutions between Christians,Jews and Muslims in the worldWe are here with attached our research report towards international peace and security for perusal and considerationsSince we are the independent and voluntary  researchers with out dependency of finance either from the government or any other agency, on the reasons that we are following Social Justice and Common Goods - Policy Paper of World Council of Churches and also By-laws of the Commission of the Churches on international affairs. Our researchers mainly follow the principles and rules laid down by the above important policy and rules.Under Articles 2.4, 3.6, 3.10&11, 8.1(b) of the By-laws of the Commission of the Churches on international affairs, we have posted our research report in United Nations Global Compact which containing of solving of problems between Christians, Jews, Muslims and Hindus in the world. In accordance with Articles 3.12 of the above By-Laws, it is a duty of commission of Churches to maintain and provide for the maintenance of contacts with International bodies such as the United Nations and its agencies include regional bodies and other non governmental Organisations, which will assist in the attainment of the aims of the Commission. The matter has being brought it to the notice of the World Churches Council and the Commission of the Churches asked its notice on the matter to the United Nations for your appropriate decisions. ?The World Churches Council Policy Paper on Social Justice and Common Goods is the best policy to the World peace and unity solutions, which has been published on 22 March 2011 and the same is in accordance with Psalm 85. The Church cannot succeed if it, isolates itself, Not only must Christians reach out to Muslims and other faiths in the spirit of ecumenism, but there is a need to embrace other people of different philosophical convictions. This requires ideological tolerance, maturity and self assurance in what one believes in. Such coalition building is made easier by choosing issues that unite organizations and movements and which have less potential causing divisions. At the same time we need an honest and inventive method of dealing with differences. The global movement for economic justice relies considerably on policy analysis and research conducted by hundreds if not thousands of academics researchers and scholars. ?Our consequences of the changing power relations in today's world is that there is more room in the public sphere for the affirmation of collective values and principles, experience proves that an informed public opinion can be powerful today, and can change governments public and international agendas. Again Churches are challenged to make use of this opportunity. They need to read the signs of time and to make their voices heard by responding to peoples cries for justice and dignity, and by speaking truth to the powers- whoever and wherever their may be. ?Christians do not have ready made answers and solutions to propose. The Bible offers guidelines (love, sharing, justice for the poor) but does not defined one "Christian" economy or "Christian" politics. ?Churches and Church related organizations can initiate public debates and largely use media means to reach a broader constituency, furthermore, regional thematic discussions can be facilitated with the ecumenical family. WCC should develop specific analysis depending on the context. ?What are theological implications for commodification common goods? ?How shall we ensure the participation all people in managing common goods in the world? ?How do we deal with power imbalances in the world? ?How can the ecumenical family engage itself effectively and in a coherent and convincing way in addressing global power imbalance? ?How can WCC lead a climate change campaign with social justice as a focus? ?What kind of collective values can be draw for the Churches to guide them in addressing the problem of commodification of common goods? ?The above questions have been answered in our research materials available at http://www.goldenduas.com and alsohttp://www.facebook.com/research of international development solutions and the same are to be discussed by the Churches, public and all its organizations in the interest of public safety, peace, unity, health, wealth, faith, interfaith ?                 Under this circumstances, it is just and necessary that UK, USA, Cambridge, Churches on the International Affairs are requested to accept our research paper and also our research organization as an organization under other faith category to assist the commission to achieve its goal of International Peace and climate changes solutions for the benefit of world community especially Christians, Jewish and Muslims, under the by-law 3.11 of CCIA. In view of the aforementioned submissions in the interest of maintenance of International Peace and Security, UN may be pleased to authorize our organization in the name and style of` Research on International Development Solutions `and also our research report in confirmatory with U/A 96 of the present Charter read with U/A 23 of the International Covenant on Economic, Social and Cultural Rights and thus render Justice.  Now, Palestine Muslims are fighting with Israel , both countries are affected and innocent people are killed frequently which is against the Quranic verses 7:137 & 5:33 that no one can claim Israel Government areas which is a place of Israel People but not Muslim or Christian and they can only Allow worship in the Holy Places of Israel . These facts has not been Discussed for amicable solutions of social justice and common good by United Nations to respect Gods word . It is pertinent to note that why the jewish people are affecting the Muslims is mention the Quran 7:167 ? And the same should be taken into consideration by jewish people in the world in the interest of social justice and common good on the light of the research paper posted  at our website www.goldenduas.com and render justice.  Your successU. Ibrahim Ali,Researcher International Development Solutions
Techstore's curator insight, September 22, 1:09 PM

Meet Strati, the first 3D printed car in the world.

#tech #technews #cartech

Gemma Shannon's curator insight, Today, 11:21 AM

What's next? 3D printed buildings?! Amazing to see how far this technology has come in such a short space of time.

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An Adorable, Tiny First Aid Kit So Anyone Can Help Rescue The Bees

An Adorable, Tiny First Aid Kit So Anyone Can Help Rescue The Bees | Science Garden | Scoop.it

Honeybees are dying around the world, and so one designer in Italy decided to create a small first aid kit in an attempt to help.

 

The Bee Saver gadget, a keychain holding a small bioplastic container of artificial nectar, is designed to be carried along on a walk. If someone sees a bee in need, they can set the container of nectar next to it. To attract the bee, the container is shaped like a flower, smells sweet, and is shaded a pleasing blue. If all goes well, the bee will take a sip and fly safely back to its hive.

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Epstein-Barr Virus Cut Out Of Infected Human Cells By CRISPR-Cas9 Genome Editing

Epstein-Barr Virus Cut Out Of Infected Human Cells By CRISPR-Cas9 Genome Editing | Science Garden | Scoop.it

Researchers at Stanford exploited the newly developed precision gene editing technology known CRISPR-Cas9 into an anti-virus technology by cutting out Epstein-Barr virus from the host genome of infected cells.  Infected cells successfully treated this way scale back proliferation caused by viral programs and engage in a self-destruct program known as “apoptosis”, or controlled cell death.  EBV is known to express a “brake” protein that suppresses apoptosis, a way to evade natural defense mechanisms.  The researchers also show importantly that there was no toxic effect on non-infected cells.

 

Epstein-Barr virus (EBV) is most often associated with mononucleosis but is also a cause of more serious conditions such as Burkitt’s lymphoma, nasopharyngeal cancer, and even autoimmune diseases.   No therapy exists but the CRISPR-Cas9 study is a valuable avenue as it overcomes two challenges posed by the virus.

 

The first challenge is during the latent stage of its life cycle it integrates into the genome and exhibits few targets for intervention. In fact most therapeutics under development are focused on attacking the virus during its active “lytic” stage so are not expected to work for cells with virus in latent stage.  In the latent stage the virus is still “on”, running a latency program that prompts the cell to proliferate.

 

The second challenge is that the virus encodes and expresses with the help of the host cell a “brake” protein BHRF1that stops the self-destruct signal stimulated by immune cells in effort to rid the body of cells that have become compromised.   The “brake” signal is one reason why EBV is frequently found in cancers: under normal conditions cells that start off on the path to cancer by acquiring mutations get stopped by the cell’s natural ability to undergo “programmed cell death” but EBV halts this process.

 

The technology for CRISPR-Cas9 entails two parts.  The first is the “cutting” enzyme, which is able to cut out pieces of viral DNA that has integrated into the host genome.  The second is a “guide RNA” which is a nucleic acid template that matches the desired target, in this case parts of the EBV sequence.  The researchers designed a CRISPR-Cas9 system that targets EBV based on its sequence in computer databases.

 

Once the cells were treated the researches found that latently infected cells no longer proliferated.  To ensure that this was not a toxic effect of treatment, the same CRISPR-Cas9 system was applied to cells that lack EBV, in which case there was no effect on proliferation.  This is an important point as some criticize CRISPR-Cas9 for its off-target effects in which unintentional cutting occurs.


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Mapping Emotions On The Body: Love Makes Us Warm All Over

Mapping Emotions On The Body: Love Makes Us Warm All Over | Science Garden | Scoop.it

Close your eyes and imagine the last time you fell in love. Maybe you were walking next to your sweetheart in a park or staring into each other's eyes over a latte.

 

Where did you feel the love? Perhaps you got butterflies in your stomach or your heart raced with excitement.

When a team of scientists in Finland asked people to map out where they felt different emotions on their bodies, they found that the results were surprisingly consistent, even across cultures.

 

 

People reported that happiness and love sparked activity across nearly the entire body, while depression had the opposite effect: It dampened feelings in the arms, legs and head. Danger and fear triggered strong sensations in the chest area, the volunteers said. And anger was one of the few emotions that activated the arms.

 

The scientists hope these body emoticons may one day help psychologists diagnose or treat mood disorders.

"Our emotional system in the brain sends signals to the body so we can deal with our situation," says Lauri Nummenmaa, a psychologist at Aalto University who led the study.

 

"Say you see a snake and you feel fear," Nummenmaa says. "Your nervous system increases oxygen to your muscles and raises your heart rate so you can deal with the threat. It's an automated system. We don't have to think about it."

 

That idea has been known for centuries. But scientists still don't agree on whether these bodily changes are distinct for each emotion and whether this pattern serves as a way for the mind to consciously identify emotions.

i

Basic emotions, such as happiness, sadness and fear, form the building blocks for more complex feelings.

Toddatkins/Wikimedia.org

To try to figure that out, Nummenmaa and his team ran a simple computer experiment with about 700 volunteers from Finland, Sweden and Taiwan.

  Read more: http://www.npr.org/blogs/health/2013/12/30/258313116/mapping-emotions-on-the-body-love-makes-us-warm-all-over?utm_content=socialflow&utm_campaign=nprfacebook&utm_source=npr&utm_medium=facebook
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Study traces ecological collapse over 6,000 years of Egyptian history

Study traces ecological collapse over 6,000 years of Egyptian history | Science Garden | Scoop.it

epictions of animals in ancient Egyptian artifacts have helped scientists assemble a detailed record of the large mammals that lived in the Nile Valley over the past 6,000 years. A new analysis of this record shows that species extinctions, probably caused by a drying climate and growing human population in the region, have made the ecosystem progressively less stable.

The study, published September 8 in Proceedings of the National Academy of Sciences (PNAS), found that local extinctions of mammal species led to a steady decline in the stability of the animal communities in the Nile Valley. When there were many species in the community, the loss of any one species had relatively little impact on the functioning of the ecosystem, whereas it is now much more sensitive to perturbations, according to first author Justin Yeakel, who worked on the study as a graduate student at the University of California, Santa Cruz, and is now a postdoctoral fellow at the Santa Fe Institute.

Around six millennia ago, there were 37 species of large-bodied mammals in Egypt, but only eight species remain today. Among the species recorded in artwork from the late Predynastic Period (before 3100 BC) but no longer found in Egypt are lions, wild dogs, elephants, oryx, hartebeest, and giraffe.

"What was once a rich and diverse mammalian community is very different now," Yeakel said. "As the number of species declined, one of the primary things that was lost was the ecological redundancy of the system. There were multiple species of gazelles and other small herbivores, which are important because so many different predators prey on them. When there are fewer of those small herbivores, the loss of any one species has a much greater effect on the stability of the system and can lead to additional extinctions."


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Microscopic Diamonds Suggest Cosmic Impact Responsible for Younger Dryas Climate Change 12,800 Years Ago

Microscopic Diamonds Suggest Cosmic Impact Responsible for Younger Dryas Climate Change 12,800 Years Ago | Science Garden | Scoop.it

A new study published in The Journal of Geology provides support for the theory that a cosmic impact event over North America some 13,000 years ago caused a major period of climate change known as the Younger Dryas stadial, or “Big Freeze.”

 

Around 12,800 years ago, a sudden, catastrophic event plunged much of the Earth into a period of cold climatic conditions and drought. This drastic climate change—the Younger Dryas—coincided with the extinction of Pleistocene megafauna, such as the saber-tooth cats and the mastodon, and resulted in major declines in prehistoric human populations, including the termination of the Clovis culture.

 

With limited evidence, several rival theories have been proposed about the event that sparked this period, such as a collapse of the North American ice sheets, a major volcanic eruption, or a solar flare.

 

However, in a study published in The Journal of Geology, an international group of scientists analyzing existing and new evidence have determined a cosmic impact event, such as a comet or meteorite, to be the only plausible hypothesis to explain all the unusual occurrences at the onset of the Younger Dryas period.

 

Researchers from 21 universities in 6 countries believe the key to the mystery of the Big Freeze lies in nanodiamonds scattered across Europe, North America, and portions of South America, in a 50-million-square-kilometer area known as the Younger Dryas Boundary (YDB) field.

 

Microscopic nanodiamonds, melt-glass, carbon spherules, and other high-temperature materials are found in abundance throughout the YDB field, in a thin layer located only meters from the Earth’s surface. Because these materials formed at temperatures in excess of 2200 degrees Celsius, the fact they are present together so near to the surface suggests they were likely created by a major extraterrestrial impact event.

 

In addition to providing support for the cosmic impact event hypothesis, the study also offers evidence to reject alternate hypotheses for the formation of the YDB nanodiamonds, such as by wildfires, volcanism, or meteoric flux.

 

The team’s findings serve to settle the debate about the presence of nanodiamonds in the YDB field and challenge existing paradigms across multiple disciplines, including impact dynamics, archaeology, paleontology, limnology, and palynology.

 


Via Dr. Stefan Gruenwald
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Bernhard H. Schmitz's curator insight, September 16, 3:33 AM

And where is the center of the YDB field?

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The Sahara Is Millions of Years Older Than Thought

The Sahara Is Millions of Years Older Than Thought | Science Garden | Scoop.it

The great desert was born some 7 million years ago, as remnants of a vast sea called Tethys closed up. The movement of tectonic plates that created the Mediterranean Sea and the Alps also sparked the drying of the Sahara some 7 million years ago, according to the latest computer simulations of Earth’s ancient climate.


Though North Africa is currently covered by the world’s largest non-polar desert, climate conditions in the region have not been constant there for the last several million years. Subtle changes in Earth’s tilt toward the sun periodically increase the amount of solar energy received by the Northern Hemisphere in summer, altering atmospheric currents and driving monsoon rains. North Africa also sees more precipitation when less of the planet’s water is locked up in ice. Such increases in moisture limit how far the Sahara can spread and can even spark times of a “green Sahara”, when the sparse desert is replaced by abundant lakes, plants and animals.

 

Before the great desert was born, North Africa had a moister, semiarid climate. A few lines of evidence, including ancient dune deposits found in Chad, had hinted that the arid Sahara may have existed at least 7 million years ago. But without a mechanism to explain how it emerged, few scientists thought that the desert we see today could really be that old. Instead, most scientists argue that the Sahara took shape just 2 to 3 million years ago. Terrestrial and marine evidence suggest that North Africa underwent a period of drying at that time, when the Northern Hemisphere started its most recent cycle of glaciation.

 

Now Zhongshi Zhang of the Bjerknes Centre for Climate Research in Bergen, Norway, and colleagues have run simulations of climate change in North Africa over the last 30 million years. Their simulations take into account changes in Earth’s orbital position, atmospheric chemistry and the ratio of land to ocean as driven by tectonic forces. The models shows that precipitation in North Africa declined by more than half about 7 million years ago, causing the region to dry out. But this effect could not be explained by changes in vegetation, Earth’s tilt or greenhouse gas concentrations—leaving tectonic action.

 

About 250 million years ago, a huge body of water called the Tethys Sea separated the supercontinents of Laurasia to the north and Gondwana to the south. As those supercontinents broke apart and shuffled around, the African plate collided with the Eurasian plate, birthing the Alps and the Himalayas but closing off the bulk of the Tethys Sea. As the plates kept moving, the sea continued to shrink, eventually diminishing into the Mediterranean.

 

What set off the aridification in Africa was the replacement of the western arm of the Tethys Sea with the Arabian Peninsula around 7 to 11 million years ago. Replacing water with land, which reflects less sunlight, altered the region’s precipitation patterns. This created the desert and heightened its sensitivity to changes in Earth’s tilt, the researchers conclude in a study published today in Nature.


Via Dr. Stefan Gruenwald
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For legume plants, a new route from shoot to root

A new study shows that legume plants regulate their symbiotic relationship with soil bacteria by using cytokinins -- signaling molecules -- that are transmitted through the plant structure from leaves into the roots to control the number of bacteria-holding nodules in the roots.

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Artificial sweeteners induce glucose intolerance by altering the gut microbiota

Artificial sweeteners induce glucose intolerance by altering the gut microbiota | Science Garden | Scoop.it

Non-caloric artificial sweeteners (NAS) are among the most widely used food additives worldwide, regularly consumed by lean and obese individuals alike. NAS consumption is considered safe and beneficial owing to their low caloric content, yet supporting scientific data remain sparse and controversial. Here we demonstrate that consumption of commonly used NAS formulations drives the development of glucose intolerance through induction of compositional and functional alterations to the intestinal microbiota. These NAS-mediated deleterious metabolic effects are abrogated by antibiotic treatment, and are fully transferrable to germ-free mice upon faecal transplantation of microbiota configurations from NAS-consuming mice, or of microbiota anaerobically incubated in the presence of NAS. We identify NAS-altered microbial metabolic pathways that are linked to host susceptibility to metabolic disease, and demonstrate similar NAS-induced dysbiosis and glucose intolerance in healthy human subjects. Collectively, our results link NAS consumption, dysbiosis and metabolic abnormalities, thereby calling for a reassessment of massive NAS usage.


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Jean-Michel Ané's curator insight, September 20, 7:16 PM

Wow... I bet that this paper will have a huge impact on the consumption of artificial sweeteners and "diet" products...  That's a fantastic study showing the importance of gut microbiome too.

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A gardener's spirit

A gardener's spirit | Science Garden | Scoop.it

Beautiful. And so true.


Via Debra Anchors
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Elaine Rakoczy's curator insight, February 1, 4:09 PM

This is great!  I hope to be like her but with a big smile!

Cheryl Steimel's curator insight, February 6, 10:49 AM

A gardener's spirit never dies.

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This air purifier is 1,000% more effective than a house plant

This air purifier is 1,000% more effective than a house plant | Science Garden | Scoop.it

Plants are nature’s inbuilt air filters - it's well known that in addition to taking in CO2 and emitting oxygen, they’re capable of eliminating toxins from the air. 

 

Back in 2007, a biomedical engineer from Harvard University partnered with a French designer to see if they could use technology to amplify that process.

 

The result is a now-commercialised device known as Andrea, an air purifier that works with any kind of living plant inside it. The system relies on the plant’s natural filtration system, but it’s 1,000 percent faster at cleaning your air than an ordinary pot plant. It currently sells for around $200, plant not included.


The battery-operated system works by using a simple fan to draw in air from the top of the device. This air is sucked by a second fan across the leaves, down through the soil and then out past a tray of water and back into the room.

 

During this process it experiences four types of natural filtration - not only do the leaves filter the air through phytofiltration, but the microbes in the plant’s roots then remove even more toxins, before the soil filters out other contaminants. Finally, it passes through the water tray at the bottom, which keeps the plant moist but also traps additional toxins.

And it looks pretty awesome too. Find out more about how it works in this video by Inhabit:

 

Source: Fast Company
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Five Photo Friday: My favorite garden insect photos of the summer - Digging The Garden

Five Photo Friday: My favorite garden insect photos of the summer - Digging The Garden | Science Garden | Scoop.it
Five Photo Friday. Here are my favorite garden insect photos. I am trying to take notice of both the insect pests and beneficial insects in my garden.
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Plant root and mycorrhizal fungal traits for understanding soil aggregation

Soil aggregation is a key ecosystem process resulting in the formation and stabilization of soil structure, consisting of soil aggregates and the resulting matrix of pore spaces. As such, it significantly alters the environment of plant roots and microbes in a multitude of ways; thus, soil structure provides the basic setting in which mycorrhizas operate and have evolved. Not surprisingly, soil aggregation is important for root growth and for a wide range of soil features and ecosystem process rates, such as carbon storage and resistance to erosion (e.g. Jastrowet al., 1998; Six et al., 2006). The aggregation of soil is a complex process, regulated by a range of abiotic factors (e.g. texture) and mediated by plants and multiple biota groups and their interactions; in spite of this complexity, plant roots and their mycorrhizal symbionts are consistently found to be a crucial force in driving soil aggregation (Six et al., 2004; Rillig & Mummey, 2006; Leifheit et al., 2014).

 
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European gene pools seems to be derived from three ancient populations

European gene pools seems to be derived from three ancient populations | Science Garden | Scoop.it

The modern European gene pool was formed when three ancient populations mixed within the last 7,000 years, Nature reports.


Blue-eyed, swarthy hunters mingled with brown-eyed, pale skinned farmers as the latter swept into Europe from the Near East. But another, mysterious population with Siberian affinities also contributed to the genetic landscape of the continent. The findings are based on analysis of genomes from nine ancient Europeans. Agriculture originated in the Near East - in modern Syria, Iraq and Israel - before expanding into Europe around 7,500 years ago.


Multiple lines of evidence suggested this new way of life was spread by a wave of migrants, who interbred with the indigenous European hunter-gatherers they encountered on the way. But assumptions about European origins were based largely on the genetic patterns of living people. The science of analysing genomic DNA from ancient bones has put some of the prevailing theories to the test, throwing up a few surprises.


In the new paper, Prof David Reich from the Harvard Medical School and colleagues studied the genomes of seven hunter-gatherers from Scandinavia, one hunter whose remains were found in a cave in Luxembourg and an early farmer from Stuttgart, Germany. The hunters arrived in Europe thousands of years before the advent of agriculture, hunkered down in southern refuges during the Ice Age and then expanded during a period called the Mesolithic, after the ice sheets had retreated from central and northern Europe.


Their genetic profile is not a good match for any modern group of people, suggesting they were caught up in the farming wave of advance. However, their genes live on in modern Europeans, to a greater extent in the north-east than in the south.

 

The early farmer genome showed a completely different pattern, however. Her genetic profile was a good match for modern people in Sardinia, and was rather different from the indigenous hunters.

But, puzzlingly, while the early farmers share genetic similarities with Near Eastern people at a global level, they are significantly different in other ways. Prof Reich suggests that more recent migrations in the farmers' "homeland" may have diluted their genetic signal in that region today.

 

Prof Reich explained: "The only way we'll be able to prove this is by getting ancient DNA samples along the potential trail from the Near East to Europe... and seeing if they genetically match these predictions or if they're different.



Via Dr. Stefan Gruenwald
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Teach Them To Fly: Make a Leaf Man

Teach Them To Fly: Make a Leaf Man | Science Garden | Scoop.it

Today we read a very fun story entitled "Leaf Man" by Lois Ehlert. Afterwards we went on a leaf hunt to see how many different kinds of leaves we could find.


Via Ron Wolford
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Ron Wolford's curator insight, September 17, 7:46 PM

Teach Them to Fly

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Team develops ultra sensitive biosensor from molybdenite semiconductor

Team develops ultra sensitive biosensor from molybdenite semiconductor | Science Garden | Scoop.it
Move over, graphene. An atomically thin, two-dimensional, ultrasensitive semiconductor material for biosensing developed by researchers at UC Santa Barbara promises to push the boundaries of biosensing technology in many fields, from health care to environmental protection to forensic industries.

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Official AndreasCY's curator insight, September 5, 1:06 AM

Seems like something out of Star Trek.

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Yale Environment 360: Tackling Climate Change Could Pay Off in as Little as 15 Years, Report Finds

Yale Environment 360: Tackling Climate Change Could Pay Off in as Little as 15 Years, Report Finds | Science Garden | Scoop.it
16 SEP 2014: TACKLING CLIMATE CHANGE COULD 
PAY OFF IN AS LITTLE AS 15 YEARS, REPORT FINDS

Limiting greenhouse gas emissions globally over the next 15 years is both economically feasible and likely to save money, according to a new report from the Global Commission on the Economy and Climate. Between 2015 and 2030, nations are expected to invest roughly $90 trillion in urban, land-use and energy infrastructure, the analysis estimated. Steering those investments toward renewable energy, efficiency improvements, and other low-emission technologies would make that global investment more costly, the panel of government and business leaders conceded — but only marginally, adding about $4 trillion overall. But these costs could eventually be offset by the lowered operating costs associated with renewable power, the report suggested. Although they are difficult to quantify, health care savings associated with improved air quality would also offset costs. According to the report, the biggest challenges for governments will be enacting stronger rules and economic policies that favor low-carbon development, such as cutting the $600 billion that countries currently spend on fossil fuel subsidies. The report highlights the plunging costs of renewable energy — solar technology costs have been cut in half since 2010, for example — and argues that limiting urban sprawl and deforestation are essential steps in combating climate change.


Via TheNaturalist
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From Poison to Passion: The Secret History of the Tomato

From Poison to Passion: The Secret History of the Tomato | Science Garden | Scoop.it
Before tomatoes became America's sweetheart, they were seen as watery, tough and possibly poisonous.

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