Opinion: Gene editing @ Gene editing will let us control our very evolution. Will we use it wisely? Dan Rather & CRISPR-cas9: a powerful tool towards precision medicine in cancer treatment @ Images about real statistics about this blog in this year & Some images about my blog @ Machine Learning That Works Like A Dream @ How to induce magnetism in graphene

https://m.phys.org/news/2019-12-magnetism-graphene.html?fbclid=IwAR2Ui9s2Ut7CaEsEoEtYX8-teKvdtPexX41vQuCMpGfTbsEXG96we0FbwIo

https://www.pioneeringminds.com/machine-learning-works-like-dream/?fbclid=IwAR0HdxsZMCQ-cTuRvNyuO1e2bW4MRwCo4ozfjdcufjKuqZjtUdZApbWPo84

https://www.nature.com/articles/s41401-019-0322-9?fbclid=IwAR1xOaUTxWbRyBwWfy-mcUcNRLrY_JcBFP4PUn7bdn-rUJl3KbvjG6HDi34

https://www.theguardian.com/commentisfree/2019/dec/08/gene-editing-will-let-us-control-our-very-evolution-we-must-use-it-wisely?fbclid=IwAR0Ker8S5JhvW325i4uiOUHLNAoKIFWo1eox__fR5xO6orRs-NBSKTzbJEI

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OpinionGene editing

Gene editing will let us control our very evolution. Will we use it wisely?

Dan Rather

I’ve covered some of the biggest stories of our age, but this is the biggest and could change what it means to be human

Sun 8 Dec 2019 08.15 GMTLast modified on Sun 8 Dec 2019 08.24 GMT

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Crispr research in a laboratory
 Crispr research: ‘It’s cheap, it’s relatively simple and it’s remarkably precise.’ Photograph: Bill Oxford/Getty Images/iStockphoto

We live in a time when science and technology are having an impact on our society in more and more ways. And the decisions that shape how these new fields of knowledge develop ultimately affect all of us.

Human Nature review – quiet revolution that began in a yoghurt pot

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When I studied biology in high school, I didn’t learn about DNA for a very simple reason. The work of Francis Crick, James Watson, Rosalind Franklin and others who unlocked the structure of the basic code of life was still years away. The idea of engineering human beings? Well, that was firmly the stuff of science fiction, like Aldous Huxley’s dystopian novel Brave New World (published a year after my birth). It seemed as likely as, say, going to the moon.

There are a few inferences you can make from this framing of my life. One is that I have been on the planet for a while. The other is the speed of change in what we know about what life is, and how we can control it, has accelerated at a rapid rate. Now we as a species are on the precipice of being able to manipulate the very building blocks of human evolution, not to mention wield unpredictable change on the greater world around us. Even as I commit that thought to paper, I pause in awe at its implications.

I have lived through eventful times and my job as a journalist has been to chronicle wars, presidents and sweeping social movements such as civil rights. I have seen a world in flux, but when I try to peer into the future I come to the conclusion that this story of humankind’s ability to understand life on its most intimate level and be able to tinker with it for our benefit or detriment is likely to be the biggest one I will ever cover.

We are living in one of the greatest epochs of human exploration and it will shape our world as profoundly as the age of the transoceanic explorers. It is just that the beachheads on which we are landing and the continents we are mapping comprise a world far too small to see with the naked eye. Some of it is even invisible to our most powerful microscopes.

Francis Crick and James Watson, co-discoverers of the double-helix structure of DNA, in Cambridge.
 Francis Crick and James Watson, co-discoverers of the double-helix structure of DNA, in Cambridge. Photograph: AP

This brings me to a term that has become a big part of my life over the last few years: Crispr. Perhaps you know of it. Perhaps you don’t. When I first heard of it, I thought it might be a new brand of toaster. I now know it’s an extremely powerful tool for editing genes in seemingly any organism on Earth, including humans. Scientists doing basic research have been uncovering the mechanisms of life for decades. They have been creating tools for modifying individual genes but Crispr is one of those revolutions where what researchers thought might be possible in the distant horizon is suddenly available now. It’s cheap, it’s relatively simple and it’s remarkably precise.

I immediately knew that this was a story that needed telling. Human Nature, the resulting film – full disclosure, I am executive producer – came out of our conversations with scientists. They tend not to be the type of people who hype things but when they talk about Crispr you can feel the urgency in their voices. This is something you need to know about. All of you. If you are worried about your health or the health of your children. If you are concerned about how we might need to engineer our planet in the face of the climate crisis. If you are in finance, law or the world of tech. This will shape all of it.

And as we grapple with the unintended consequences of the internet and social media, as we try to make progress against a heating planet, I humbly submit that we as a species tend not to be good at thinking through where we are going until a crisis is already upon us. I fervently hope with Crispr that we can start the conversation sooner. That we can start it now. That’s why we made the film.

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To be clear, we are probably a long way from designing babies to be more intelligent or more musically inclined. Life is just too complex for that, at least right now. More immediately, there is so much about this technology that is very exciting. As someone who remembers a time when my classmates were struck down with childhood diseases for which we now have vaccines, I know science can have profound applications for human health. Crispr could cure genetic diseases such as sickle cell and Huntington’s. It is being tested against cancers and HIV. It could also potentially be used to make crops more drought-resistant or food more nutritious.

On the other hand, we are walking closer to a world Aldous Huxley foresaw. What does it mean to be human? Where should we draw the boundaries beyond which we dare not cross? The inspiring researchers we talked to for the film know that the ethical and moral questions this technology raises are not for them to decide. Science has given us the tools, but not the answers. This is up to us, all of us. We need to be informed. We need to be honest with what’s real and what’s not. And we need to add our voices to a global conversation. That’s part of our responsibility as humans living on Earth today.

Dan Rather is one of the US’s most feted journalists. He anchored CBS Evening News for 24 years

Human Nature is in UK cinemas now before a university town tour in the new year, wondercollaborative.org/human-nature-documentary-film/#screenings It will be shown on BBC Storyville in spring/summer 2020

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  • Guardian PickAny talk of practical applications for molecular biology technologies is way premature. Off target effects common in gene editing methods will not be removed for a long time to come, and I cannot for the life of me understand why scientific reporting is so uncritical. As a Molecular biologist and now Professor of Molecular Medicine I have worked with molecular techniques for the last 40 years and even basic methods such as PCR, reverse transcript…Jump to commentStephenBustin15h ago1516
  • Guardian PickAgain, an article implying that CRISPR can affect intelligence or creativity.It cannot.CRISPR edits one specific gene section. That is all.We do not have an “Intelligence” gene section. Therefore CRISPR cannot promote intelligence. Ditto “Musicality” or “Beauty”.If, however, you want your foetus to have blue eyes instead of brown, then eventually you might be able to do that.Eventually, if we do manage to lock down the sequences for resistan…Jump to commentSethis215h ago1516

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CRISPR-cas9: a powerful tool towards precision medicine in cancer treatment

Acta Pharmacologica Sinica (2019)Cite this article

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Abstract

Cancer is a highly heterogeneous disease in term of molecular signature even though it is originated from the same tissue type. Cancer heterogeneity may occur during its development or treatment, which is the main cause resulting in drug resistance and recurrence. Precision medicine refers to matching the right medicine to the right patients based on their molecular signatures. Therefore, a thorough understanding of the mechanism of tumorigenesis and drug resistance is essential to precision medicine. CRISPR-cas9 system is a powerful tool for gene editing and CRISPR-based high-throughput screening has been widely applied especially in searching for tumor-driven or synergistic lethal genes aiming to overcome drug resistance. In this review, we describe the progress of CRISPR-cas9-based unbiased screening in precision medicine including identification of new drug targets, biomarkers and elucidation of mechanisms leading to drug resistance. The existing challenges as well as the future directions are also discussed.

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Acknowledgements

This work was supported by the “Personalized Medicine Molecular Signature-based Drug Discovery and Development” Strategic Priority Research Program of the Chinese Academy of Sciences [XDA12020111], the National Science and Technology Major Project “Key New Drug Creation and Manufacturing Program” [2018ZX09711002-011-014 & 2018ZX09711002-004-011] and the National Natural Science Foundation of China [81773760]. It was also partially supported by the Fudan-SIMM Joint Research Fund [FU-SIMM20172005].

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Affiliations

  1. Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
    • Hui Xing
    •  & Ling-hua Meng
  2. University of Chinese Academy of Sciences, Beijing, 100049, China
    • Hui Xing
    •  & Ling-hua Meng

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Correspondence to Ling-hua Meng.

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Xing, H., Meng, L. CRISPR-cas9: a powerful tool towards precision medicine in cancer treatment. Acta Pharmacol Sin (2019) doi:10.1038/s41401-019-0322-9

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Keywords

  • precision medicine
  • CRISPR-cas9
  • drug target
  • biomarker
  • drug resistance
  • synergistic lethality

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Machine Learning That Works Like A Dream

Machine Learning That Works Like A Dream

A group of researchers have created a new artificial intelligence program for automatically classifying the sleep stages of mice that combines two popular machine learning methods. Dubbed “MC-SleepNet,” the algorithm achieved accuracy rates exceeding 96% and high robustness against noise in the biological signals. The use of this system for automatically annotating data can significantly assist sleep researchers when analyzing the results of their experiments.

Scientists who study sleep often use mice as animal models to better understand the ways the activity in the brain changes during the various phases. These phases can be classified as awake, REM (rapid eye movement) sleep, and non-REM sleep. Previously, researchers who monitored the brainwaves of sleeping mice ended up with mountains of data that needed to be laboriously labeled by hand, often by teams of students. This represented a major bottleneck in the research.

Now, they have introduced a program for automatically classifying the stage of sleep that a mouse experienced based on its electroencephalogram (EEG) and electromyogram (EMG) signals, which record electrical activity in the brain and body, respectively.

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How to induce magnetism in graphene

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How to induce magnetism in graphene

 December 10, 2019 by Karin Weinmann, Swiss Federal Laboratories for Materials Science and Technology

How to induce magnetism in graphene
3-D-rendered high-resolution scanning tunneling micrograph of Clar’s goblet. Credit: Empa

Graphene, a two-dimensional structure made of carbon, is a material with excellent mechanical, electronic and optical properties. However, it did not seem suitable for magnetic applications. Together with international partners, Empa researchers have now succeeded in synthesizing a unique nanographene predicted in the 1970s, which conclusively demonstrates that carbon in very specific forms has magnetic properties that could permit future spintronic applications. The results have just been published in the renowned journal Nature Nanotechnology.

Depending on the shape and orientation of their edges, graphene nanostructures (also known as nanographenes) can have very different properties—for example, they may exhibit conducting, semiconducting or insulating behavior. However, one property has so far been elusive: magnetism. Together with colleagues from the Technical University in Dresden, Aalto University in Finland, Max Planck Institute for Polymer Research in Mainz and University of Bern, Empa researchers have now succeeded in building a nanographene with magnetic properties that could be a decisive component for spin-based electronics functioning at room temperature.

Graphene consists only of carbon atoms, but magnetism is a property hardly associated with carbon. So how is it possible for carbon nanomaterials to exhibit magnetism? To understand this, we need to take a trip into the world of chemistry and atomic physics.

The carbon atoms in graphene are arranged in a honeycomb structure. Each carbon atom has three neighbors, with which it forms alternating single or double bonds. In a single bond, one electron from each atom—a so-called valence electron—binds with its neighbor; while in a double bond, two electrons from each atom participate. This alternating single and double bond representation of organic compounds is known as the Kekulé structure, named after the German chemist August Kekulé who first proposed this representation for one of the simplest organic compound, benzene (Figure 1). The rule here is that electron pairs inhabiting the same orbital must differ in their direction of rotation—the so-called spin—a consequence of the quantum mechanical Pauli’s exclusion principle.

“However, in certain structures made of hexagons, one can never draw alternating single and double bond patterns that satisfy the bonding requirements of every carbon atom. As a consequence, in such structures, one or more electrons are forced to remain unpaired and cannot form a bond,” explains Shantanu Mishra, who is researching novel nanographenes in the Empa nanotech@surfaces laboratory headed by Roman Fasel. This phenomenon of involuntary unpairing of electrons is called “topological frustration” (Figure 1).

How to induce magnetism in graphene
Left: Illustration of Clar’s goblet as a cut-out of graphene. Right: Illustration of the Kekulé structures of benzene (top) and the impossibility of drawing Kekulé structures for Clar’s goblet without leaving unpaired electrons (bottom). Credit: Empa

But what does this have to do with magnetism? The answer lies in the “spins” of the electrons. The rotation of an electron around its own axis causes a tiny magnetic field, a magnetic moment. If, as usual, there are two electrons with opposite spins in an orbital of an atom, these magnetic fields cancel each other. If, however, an electron is alone in its orbital, the magnetic moment remains—and a measurable magnetic field results.

This alone is fascinating. But in order to be able to use the spin of the electrons as circuit elements, one more step is needed. One answer could be a structure that looks like a bow tie under a scanning tunneling microscope (Figure 2).

Two frustrated electrons in one molecule

Back in the 1970s, the Czech chemist Erich Clar, a distinguished expert in the field of nanographene chemistry, predicted a bow tie-like structure known as “Clar’s goblet” (Figure 1). It consists of two symmetrical halves and is constructed in such a way that one electron in each of the halves must remain topologically frustrated. However, since the two electrons are connected via the structure, they are antiferromagnetically coupled—that is, their spins necessarily orient in opposite directions.

In its antiferromagnetic state, Clar’s goblet could act as a “NOT” logic gate: if the direction of the spin at the input is reversed, the output spin must also be forced to rotate.

How to induce magnetism in graphene
Left: Experimental high-resolution scanning tunneling micrograph of Clar’s goblet. Right: Ball-and-stick model of Clar’s goblet (carbon atoms: gray, hydrogen atoms: white) with overlaid spin density distribution in the antiferromagnetic ground state (blue: spin up, red: spin down). Credit: Empa

However, it is also possible to bring the structure into a ferromagnetic state, where both spins orient along the same direction. To do this, the structure must be excited with a certain energy, the so-called exchange coupling energy, so that one of the electrons reverses its spin.

In order for the gate to remain stable in its antiferromagnetic state, however, it must not spontaneously switch to the ferromagnetic state. For this to be possible, the exchange coupling energy must be higher than the energy dissipation when the gate is operated at room temperature. This is a central prerequisite for ensuring that a future spintronic circuit based on nanographenes can function faultlessly at room temperature.

From theory to reality

So far, however, room-temperature stable magnetic carbon nanostructures have only been theoretical constructs. For the first time, the researchers have now succeeded in producing such a structure in practice, and showed that the theory does correspond to reality. “Realizing the structure is demanding, since Clar’s goblet is highly reactive, and the synthesis is complex,” explains Mishra. Starting from a precursor molecule, the researchers were able to realize Clar’s goblet in ultrahigh vacuum on a gold surface, and experimentally demonstrate that the molecule has exactly the predicted properties.

Importantly, they were able to show that the exchange coupling energy in Clar’s goblet is relatively high at 23 meV (Figure 2), implying that spin-based logic operations could therefore be stable at room temperature. “This is a small but important step toward spintronics,” says Roman Fasel.

More information: S. Mishra, et al. Topological frustration induces unconventional magnetism in a nanographene, Nature Nanotechnology (2019).

Journal information: Nature Nanotechnology

Provided by Swiss Federal Laboratories for Materials Science and Technology

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Phys.org™ (formerly Physorg.com) is a leading web-based science, research and technology news service which covers a full range of topics.

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  1. Good day! This is my first comment here so I just wanted to give a quick shout out and tell you I really enjoy reading through your blog posts. Can you suggest any other blogs/websites/forums that go over the same subjects? Appreciate it!

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