CRISPR opens door to new type of medicine—’genome surgery’

October 26, 2018, University of California – Berkeley
CRISPR opens door to new type of medicine—‘genome surgery’
Delaney Van Riper, 19, was born with a rare disease called Charcot-Marie-Tooth (CMT). Credit: Steve Babuljak

Within a few years, Jim Johnsen and Delaney Van Riper may be among the first to benefit from CRISPR-Cas9 gene editing, a breakthrough that has already revolutionized biology research and promises to resurrect gene therapy.

UC San Francisco doctors working closely with UC Berkeley scientists plan to edit their genomes to correct rare genetic mutations and slow or halt progression of their diseases.

If successful, the trials will inaugurate a new era of “genome surgery”—the precision targeting of genetic defects in the genome, using CRISPR-Cas9 customized to individual patients. Such “bespoke” therapies can benefit small groups of individuals or families with particular genetic defects that would never be addressed by large pharmaceutical companies.

Johnsen and his family, including his daughter Greta, are carriers of a rare disorder, Best disease, that afflicts perhaps a thousand people nationwide and leads to early vision loss and eventual blindness, much like the more common macular degeneration.

Van Riper was born with a rare disease called Charcot-Marie-Tooth, which gradually destroys her nerve cells’ ability to relay messages between her brain and muscles, causing her to slowly lose control of her limbs and her muscles to waste.

IGI researchers, including Bruce Conklin of UCSF and Jennifer Doudna of UC Berkeley, discuss the promise of CRIRSP-Cas9 ‘genome surgery.’ Credit: UCSF video

CRISPR-Cas9, invented at UC Berkeley, could make treating such diseases, if not easy, at least straightforward: with a large enough CRISPR toolbox, doctors can pick and choose the best approach and tailor a therapy to the specific genetic mutation.

“Imagine a world where people go to the doctor, and they get their genome sequenced and learn they have a genetic disorder,” says CRISPR-Cas9 inventor Jennifer Doudna, who pioneered the first CRISPR applications in her UC Berkeley lab in 2012. “And instead of telling them they need to live with that disorder, we have the technology that can actually treat them  –  potentially even cure them.”

Doudna is quoted in an article that highlights the collaboration among scientists in the Innovative Genomics Institute, a joint UCSF/UC Berkeley research initiative that seeks to expand the CRISPR toolbox and make CRISPR-Cas9 gene editing more precise, more effective and safer. Doudna is IGI’s executive director, and is also a Howard Hughes Medical Institute investigator and Berkeley professor of molecular and cell biology and of chemistry.

While Johnsen and Van Riper have yet to be treated, both have donated their cells to Bruce Conklin at UCSF, where they have been coaxed into becoming stem cells that are now being treated with CRISPR-based  to, ideally, correct their mutations. Once this is successful in the lab, the stem cells will be injected into the eye, in Johnsen’s case, or muscles, in Van Riper’s case, in hopes of alleviating their symptoms.

CRISPR opens door to new type of medicine—‘genome surgery’
Jim Johnsen, seated, meets with Po-Lin So, Bruce Conklin and Angela Liu at the Gladstone Institutes to discuss his rare eye disease. Credit: UCSF

The researchers acknowledge that Best  and CMT are simpler targets than many genetic diseases: both are caused by single nucleotide changes in a single gene, making it simpler to fix; and the symptoms occur in tissues that are relatively easy to access. Nevertheless, treatments like this will pave the way for treating more complex genetic diseases.

“Almost universally, the first targets of genome surgery will be incurable diseases, where there is truly no other option,” says Conklin, a senior investigator at the Gladstone Institutes, UCSF professor of medicine and deputy director of IGI. “If we can treat these, it will open the door to a new type of medicine.”

 Explore further: Genome damage from CRISPR/Cas9 gene editing higher than thought

Gravitational waves could shed light on dark matter

October 22, 2018, University of Zurich
Gravitational waves could shed light on dark matter
Snapshots of the 120 million particle simulation of two merging dwarf galaxies, which each contain a blackhole, between 6 and 7.5 billion years. Credit: UZH

The forthcoming Laser Interferometer Space Antenna (LISA) will be a huge instrument allowing astronomers to study phenomena including black holes colliding and gravitational waves moving through space-time. Researchers from the University of Zurich have now found that LISA could also shed light on the elusive dark matter particle.

The Laser Interferometer Space Antenna (LISA) will enable astrophysicists to observe  emitted by  as they collide with or capture other black holes. LISA will consist of three spacecraft orbiting the sun in a constant triangle formation. Gravitational waves passing through will distort the sides of the triangle slightly, and these minimal distortions can be detected by laser beams connecting the spacecraft. LISA could therefore add a new sense to scientists’ perception of the universe and enable them to study phenomena invisible in different light spectra.

Scientists from the Center for Theoretical Astrophysics and Cosmology of the University of Zurich, together with colleagues from Greece and Canada, have now found that LISA will not only be able to measure these previously unstudied waves, but could also help to unveil secrets about dark matter.

Dark matter particles are thought to account for approximately 85 percent of the matter in the universe. However, they are still only hypothetical—the name refers to their elusiveness. But calculations show that many galaxies would be torn apart instead of rotating if they weren’t held together by a large amount of dark matter.

That is especially true for dwarf galaxies. While such galaxies are small and faint, they are also the most abundant in the universe. What makes them particularly interesting for astrophysicists is that their structures are dominated by dark matter, making them natural laboratories for studying this elusive form of matter.

Black holes and dark matter are connected

In a new study reported in Astrophysical Journal Letters, UZH Ph.D. student Tomas Ramfal conducted high-resolution computer simulations of the birth of dwarf galaxies, yielding surprising results. Calculating the interplay of dark matter, stars and the central black holes of these galaxies, the team of scientists from Zurich discovered a strong link between the merger rates of these black holes and the amount of dark matter at the center of dwarf . Measuring gravitational waves emitted by merging black holes can thus provide hints about the properties of the hypothetical .

The newly found connection between black holes and  can now be described in a mathematical and exact way for the first time. Lucio Mayer, the group leader, says, “Dark  is the distinguishing quality of . We had therefore long suspected that this should also have a clear effect on cosmological properties.”

The connection comes at an opportune moment, as preparations for the final design of LISA are under way. Preliminary results of the researchers’ simulations were met with excitement at meetings of the LISA consortium. The physics community sees the new use of gravitational wave observations as a promising new prospect for one the biggest future European space missions, which is expected to launch in about 15 years and could link cosmology and particle physics—the incredibly big and the unimaginably small.

 Explore further: Is dark matter made of primordial black holes?

More information: Tomas Tamfal et al, Formation of LISA Black Hole Binaries in Merging Dwarf Galaxies: The Imprint of Dark Matter, The Astrophysical Journal (2018). DOI: 10.3847/2041-8213/aada4b

A tiny antenna could be good for your health—all you have to do is stick it in your brain

October 11, 2018 by Laura Castañón, Northeastern University
A tiny antenna could be good for your health—all you have to do is stick it in your brain
Credit: Northeastern University

Antennas have come a long way from the rabbit ears on your old TV. But the antenna that Northeastern doctoral student Hwaider Lin has been working on since 2015 is about 100 times smaller than the one currently in your smartphone.

Lin said the antenna he is developing could eventually be used in a chip implanted in a patient’s brain to help treat disorders such as depression or severe migraines. Currently, researchers use electromagnetic currents created outside a patient’s head to stimulate neurons in the brain to help treat these medical conditions. But this method is imprecise. With a smaller antenna, researchers may be able to create an implant in the brain that would more precisely target specific neurons.

Lin’s antenna recently won first prize in design a contest run by the publishers of NASA Tech Briefs magazine. More than 800 applicants from 60 different countries submitted their technology to the “Create the Future Design Contest,” which judges feats of innovative engineering in seven different categories. Lin topped the category for Electronics/Sensors/Internet of Things.

“I’m kind of surprised I got the first prize,” Lin said. “But I think [the antenna] is worth it.”

Conventional antennas send signals by bouncing electrons back and forth along a metal cable. This creates waves of electromagnetic radiation that can be picked up by other antennas tuned to the right frequency. Changing the size of the antenna changes the frequency. There’s a limit to how small these antennas can be before they stop being effective.

The antenna Lin has been working on starts with a different kind of wave: an acoustic one. Acoustic waves are slow-moving physical vibrations. Because of their slower speed, they can match the frequency of an electromagnetic wave, but will have a wavelength that is thousands of times smaller. This means the antenna can be smaller too.

A tiny antenna could be good for your health—all you have to do is stick it in your brain
Credit: Northeastern University

Lin’s antenna is able to translate those acoustic waves into faster-moving electromagnetic ones with the same frequency. This is because the material vibrating in Lin’s antenna is magnetic.

“We actually do materials science first,” said Lin, who works in Northeastern’s Advanced Materials and Microsystems Lab. “Our material is the most important thing for this antenna.”

This work was first published in August 2017 in Nature Communications. Since then, Lin and his advisor, Northeastern professor Nian Sun, have been refining it to be used in different applications.

“So far, the best choice is biomedical applications,” Lin said. “They need a really small  that can receive power and transmit information back to the computer outside.”

The team recently started working with a group at Harvard Medical School to find ways to use this technology in medical implants. Together, they have the potential to design new devices to sense what is going on in the brain, stimulate different areas, and communicate important information back to researchers.

But first, Lin will be flying to a reception in New York to receive his prize from NASA Tech Briefs: a high-end computer that can handle the complicated simulations his work requires.

“This event is very special,” Lin said. “They see the potential of this technology.”

 Explore further: New membrane-based antenna much smaller than conventional ones

More information: Tianxiang Nan et al. Acoustically actuated ultra-compact NEMS magnetoelectric antennas, Nature Communications (2017). DOI: 10.1038/s41467-017-00343-8

Read more at:

Cheap but powerful Raspberry Pi rival: $45 NanoPi Neo4 is six-core Android board with USB 3.0 and 4K support

​The NanoPi Neo4 is the cheapest six-core, single-board computer to be released, but there’s a catch.

The NanoPi Neo4 is the cheapest six-core, single-board computer to be released, boasting relatively modern features like USB 3.0 and support for 4K displays.

But there’s a catch, the board may only cost $45, only $10 more than the Raspberry Pi 3 B+, but it only comes with 1GB of memory.

This limited amount of DDR3 RAM will likely bottleneck the board’s RK3399 system on a chip (SoC), which packs the Arm-based dual-core A72 and quad-core A53 processors.

If you can work within limitations of the memory, the board also supports reasonably fast data transfer via its USB 3.0 and Gigabit Ethernet ports, as well as one USB 2.0 Type-C port. Additionally, there’s potential for adding fast SSD storage via a PCIe x2 interface.

The Neo4 outputs to 4K displays via HDMI 2.0 and supports 4K 60FPS playback of VP9- and H265/H264-encoded video, although smooth playback may be undercut by the 1GB memory.

These specs outstrip the Pi 3 B+ in most respects, and while Pi 3 B+ has the same amount of memory as the Neo4, the NanoPi board uses faster DDR3 memory than the DDR2 found on the Pi. However, the Pi 3 B+ does have more populated Type-A USB ports, with four on the Pi compared to two on the Neo4. The Pi 3 B+ also supports faster Wi-Fi, 802.11ac (Wi-Fi 5) compared to 802.11n (Wi-Fi 4) on the Neo4.

The Neo4 supports a range of Linux-based operating systems, including a custom version of Ubuntu 18.04, Lubuntu 16.04 and Android 8.1 (if you buy an additional 16GB eMMC module for $12).

The board’s makers say the NanoPi Neo4 is suited to developing a wide range of software and hardware. The NanoPi Neo4 shares the same 40-pin header layout as the Raspberry Pi, but is smaller than the Pi 3 B+, measuring just 60mm x 45mm.

An early review of the board says it could be a “perfect pocket server” but mentions the difficulty in housing the Neo4’s massive heatsink in a case, as well the need for an additional fan for cooling if you are planning sustained heavy use. It also mentions that it’s difficult to hook hardware to the Neo4’s PCIe x2 interface at present, due to the lack of compatible add-on boards.

As with most single-board computers, it’s worth noting that few boards are as accessible or offer the same breadth of stable software as the Pi. Some users of recent NanoPi boards have also encountered driver problems and system setup issues, so this board may be one for the more technically proficient.


Image: Friendly Elec

Read more

If you’re in the market for a portable projector, Anker has a line of portable projectors available under the Nebular brand. We had the chance to test out the company’s Nebular Mars II portable projector, which allows movie goers to throw a giant screen on the wall, anywhere in their home or on the road.

The Nebular Mars II offers 720p high definition picture quality (1280 x 720 resolution) with DLP technology and has 300 lumens of brightness. It has quick 1-second autofocus and runs a custom fork of Android 7.1.

Inside the box, you’ll find the Mars II projector itself, a remote control and AC adapter to go with the instruction booklet. The projector is a Red Dot design award winner for 2018. The unit itself comes with a leather-like carrying handle and has control buttons along the top and input along the back. There’s a built-in lens cap as well.

IMG 0249

Controls along the top allow for quick access to volume, back, and Bluetooth. The Mars II can act as a Bluetooth speaker and also has a built-in battery, allowing for ultimate portability. It also has built-in Wi-Fi to connect to whatever wireless network is available. No network available? The USB port allows you to play videos from any USB stick or hard drive.

IMG 0250

On the back you’ll see the DC in port, HDMI, USB and audio out:

IMG 0251

Here is what the projector lens looks like—the lens cap slides down:

IMG 0252

The remote is easy to control the Mars II projector, but using Anker’s Nebula Connect iOS app is highly recommended, to make it easier to login to services such as Netflix, Amazon Prime Video and more.

Below is what the Mars II home screen looks like, with quick shortcuts to install Amazon Prime Video, YouTube and Netflix. You can also access HDMI which means you can play any console with the Mars II as well.

56081947450 896FDE47 E490 449C A5C7 69F1ED4A67A9

Picture quality is actually not bad considering the size of this portable projector. Watching YouTube presented some decent images along our bedroom wall:

IMG 0256

The Nebular Mars II can project 30 inches to 150 inches on a wall in 720p. Below is the largest image we could make in our room and if you have decent expectations, the quality is still very good for making your own portable home theatre.

IMG 0266

One of the most surprising aspects of the Mars II was its dual 10w speakers, which were quite loud and clear, able to easily fill the room. They helped drown out some of the fan noise from the projector as well, if you have it placed close to you.

The projector’s autofocus is fast too, as it will display a bullseye ring for it to quickly refocus itself should you bump or move the unit.

IMG 0262

We tested the Anker Nebular Mars II portable projector in a pitch black room with blackout blinds and it looked great on the wall. But in daylight, the projector doesn’t show up as well, so it’s best to try it in darker environments.

The Mars II also supports Apple AirPlay, and we were able to connect to the device to beam our iPhone home screen and whatever we were playing on our device.

You can use the Mars II on its built-in battery, which Anker says can support up to 4 hours of video. We didn’t fully test the limits of the battery, but this should easily last you at least a movie or two (or about 1x Titanic and another third of a second marathon viewing).

If you’ve been tempted to buy a portable projector, take a look at the Anker Nebular Mars II. It has fast autofocus, great picture in the dark, decent speakers for the size and also its HDMI port means unlimited possibilities. It’s also fairly easy to use and not overly-complicated to get set up and running out of the box. This portable projector will definitely impress your friends and family at your next BBQ or camping trip. I can also see it being useful for work presentations, without the need for a power outlet.

As for a negative, it’s definitely the price of the Mars II portable projector, which is a whopping $1049 CAD on That’s a huge investment to spend on a portable projector, but if you need one that can go anywhere, plus supports AirPlay, USB and HDMI, the Nebular Mars II may fit the bill.

Researchers modify CRISPR to reorganize genome

October 11, 2018, Stanford University Medical Center
CRISPR-associated protein Cas9 (white) from Staphylococcus aureus based on Protein Database ID 5AXW. Credit: Thomas Splettstoesser (Wikipedia, CC BY-SA 4.0)

Researchers at Stanford University have reworked CRISPR-Cas9 gene-editing technology to manipulate the genome in three-dimensional space, allowing them to ferry genetic snippets to different locations in a cell’s nucleus.

The new technique, dubbed CRISPR-genome organization or simply CRISPR-GO, uses a modified CRISPR protein to reorganize the genome in three dimensions. If CRISPR is like molecular scissors, then CRISPR-GO is like molecular tweezers, grabbing specific bits of the genome and plunking them down in new locations of the nucleus. But it’s more than just physical relocation: Displacing genetic elements can change how they function.

The research sheds new light on how the genome’s spatial organization in the nucleus governs the function of the cell overall.

“The question of why spatial organization in a cell matters is an important one, and it’s also not one that scientists agree on,” said Stanley Qi, Ph.D., assistant professor of bioengineering and of chemical and systems biology. “CRISPR-GO could provide an opportunity to answer that question by enabling us to target, move and relocate very specific stretches of DNA, and see how their new placements in the nucleus change how they function.”

Most mammalian cells contain a nucleus that houses more than 6 feet of DNA, if stretched out in a line. This genetic material determines the fate of the cells and, if out of place or damaged, can lead to disease. Previous studies have shown that DNA tends to clump in certain areas in the nucleus. How that placement affects the DNA’s function, however, is still unclear.

In the proof-of-principle study, Qi investigated three distinct subregions of the nucleus using CRISPR-GO, testing an overarching hypothesis: Do genes and other  behave differently in different zones of the nucleus?

So far, their data show that specific compartments and some free-floating bodies of proteins in the nucleus can sway the function of repositioned DNA. Depending on where the genetic materials are located, some nuclear regions repress gene expression and some accelerate telomere growth, and subsequently cell division. One protein body may even hold the power to suppress .

A study detailing this research will be published online Oct. 11 in Cell. Qi is the senior author. Postdoctoral scholar Haifeng Wang, Ph.D., is the lead author.

Bridging the gap

Demystifying the physical details of the genome has proved to be a tedious task, but there are some existing technologies that allow scientists to peer into  and see how their guts are physically organized. What’s been missing is a way to tamper with this organization. CRISPR-GO is the first to offer researchers a means to do so.

By decommissioning the “cutting” mechanism of CRISPR-Cas9, the editing tool becomes more of a delivery system, which Qi used to deliver small stretches of DNA via a programmable guide RNA to a new location in the nucleus.

There are three essential parts of CRISPR-GO. First, there’s what Qi calls the “address” of the genetic target that you want to relocate—a stretch of DNA that’s targeted with a complementary strand of binding RNA. Then, you need the destination’s address—the specific portion of DNA in a nuclear compartment to which you want to move the chromatin. Finally, there’s the “bridge,” which, in this case, is a catalyst that sparks the congealing of the target DNA to its new home in the nucleus.

“Kids often like to build little railroads to help trains get from one station to another,” said Qi. “It’s not so different from what we’re doing here.”

Different room, different function

Qi describes the functionalities of the nuclear compartments like the spaces of a house. In every room of your home, you do different things—in the kitchen, you cook; in the bedroom, you sleep. In the nucleus of a cell, the same concept applies. There are multiple compartments in the nucleus that all have specific roles in upholding cell functionality overall. Qi and his lab investigated three distinct areas of the nucleus, testing whether they could somehow shift the function of chromatin depending on where they moved it.

By using CRISPR-GO, the researchers observed that genes relocated to a part of the nucleus called the Cajal body, an amorphic and somewhat mysterious blob of proteins and RNA, stopped expressing proteins.

“We were super-excited to see this; it’s the first time that researchers have evidence to show the Cajal body can have a direct gene-regulation effect, in this case repressing gene expression,” Qi said. “It suggests that the Cajal body has some unexpected role in controlling transcription.” That could be big, as transcription is an important process that synthesizes the “code” for protein production.

When Qi used CRISPR-GO to move the DNA of telomeres—the molecular caps of chromosomes that are associated with longevity—from the middle to the edge of the nucleus, the telomeres stopped growing, halting the cell cycle and reducing cell viability. The opposite, however, happened when telomeres were moved closer to the Cajal body: They grew and, in doing so, increased cell viability.

The third application used CRISPR-GO to form a promyelocytic leukemia body. This glob of proteins is known to suppress pro-tumor genes. By positioning it next to cancer-causing genes in the , Qi plans to test if it can help curb tumor formation.

“Another unique advantage of CRISPR-GO is that we can track the interactions between chromatin DNA and nuclear compartments in real time under a microscope,” Wang said.

While the evidence shown by CRISPR-GO is exciting, the research is still in a pilot stage, and there’s more work to be done before the findings can be confirmed, Qi said.

“We’re very excited about the potential here and, while we’ve answered a couple questions, we’ve opened up about 20 more,” Qi said.

It will be even more important to decipher why these location-based effects take place in specific nuclear compartments, and what the underlying cause is, he said. One day, Qi hopes, this line of research will come to bear on human health.

 Explore further: Researchers show that nucleosomes can inhibit CRISPR-Cas9 cleavage efficiency

Save $130 on a coffee maker that works with Alexa


Best Coffee Maker On AmazonIt took a long time for “smart home” gadgets to actually become “smart,” and the world has Alexa to thank. Amazon’s voice assistant pretty much changed the world, giving electronics companies a free way to integrate voice control into their devices. These days, it almost seems silly to buy a device that doesn’t have Alexa integration, and that goes for coffee makers, too. Check out the Behmor Connected Customizable Temperature Control Coffee Maker, which has a bunch of smart features and can be controlled by Alexa. You’ll wonder how you ever lived without it.

Here are some highlights from the product page:

  • Customizable, temperature control coffee maker with phone app for easy, remote operation that allows you to control brewing temperature, pre-soak time and altitude for precision brewing
  • Integrated with Amazon Alexa – all you need is your voice to make a morning cup of coffee; World’s first Specialty Coffee Association (SCA) certified smart brewer
  • Connection with Amazon Dash Replenishment that will automatically reorder beans or grounds, ensuring that you never run out of coffee again
  • Create your favorite brewing profile and save to favorites or select from app’s library (works on Apple iOS 7 and higher and Android 4.0+ and higher). The Start button on the front of the brewer allows you to quick start brewing without the app
  • The pulsed water flow design ensures that all grounds are fully saturated and the pre-soak function adds water to the grounds before brewing allowing the coffee to fully bloom
  • Temperature control from 190°-210° F with altitude calibration is critical for ideal coffee extraction; recommended water temperature is between 195° and 205° F
  • Double walled stainless carafe maintains optimal coffee temperature and keeps coffee hot for hours

Google Home will let you adjust podcast playback speed

“Hey Google, play twice as fast.”

Raspberry Pi’s Raspbian OS Updated With New Kernel, Startup Wizard Improvements
Written by Michael Larabel in Operating Systems on 11 October 2018 at 09:56 AM EDT.

Raspberry Pi’s Debian-based Raspbian OS has been updated today with four months worth of improvements for this popular ARM SBC.

One of the most user-facing changes with the new Raspbian 2018-10-09 update are startup wizard improvements. This initial-run wizard will now install more language support packages, improves keyboard-only workflows when having no mouse, network connectivity handling enhancements, an IP address indicator, and other improvements to make a better out-of-the-box experience.

This Raspbian update also is using the Linux 4.14.71 kernel compared to 4.14.50 on the older build from this summer. There are also a slew of package updates from a newer RealVNC server, now bundling libav-tools, dropping Mathematic, and other packaging changes.

Raspbian 2018-10-09 also has support for the Raspberry Pi PoE HAT, updated firmware images, hardware acceleration support for FFmpeg, support for DHCPCD with 3G network devices, and a variety of other updates.

The new Raspbian 2018-10-09 installation image is available as always from

Deep learning? Here’s how to exercise your neural networks

Getting practical with machine learning and AI

There are many ways machines can learn, but for humans nothing beats getting together with like-minded souls who’ve trodden a similar path.

So if you’re looking to sharpen up your work in machine learning, artificial intelligence or data science, you should be joining us on Monday morning when we open the doors to Minds Mastering Machines.

We’ve assembled a lineup of speakers who can take you from the fundamentals through to the practical application of key technologies and techniques including TensorFlowKerasLime, GPUs, Deep Learning and Reinforcement Learning.

And they’ll be discussing how they’ve applied them in areas such as financial tradingmilitary vehiclesarchitectural engineering, and just keeping the trains running.

We also have some spaces left in our brace of workshops covering developing and deploying machine learning and using the cloud, containers and DevOps to get your project into production.

This all happens at 30 Euston Square on October 15 to 17, and because this conference is brought to you by The Register and Heise, you can ensure that the conversation will flow at lunch, and at our first night drinks party.

But time is running out. Head to the MCubed website today, and secure your place. See you next week.