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  • richardmitnick 12:24 am on July 2, 2018 Permalink | Reply
    Tags: , C6orf106 or "C6", , , DNA, Gene discovery unlocks mysteries of our immunity, , Our immune system   

    From Commonwealth Scientific and Industrial Research Organisation CSIRO: “Gene discovery unlocks mysteries of our immunity” 

    CSIRO bloc

    From Commonwealth Scientific and Industrial Research Organisation CSIRO

    7.1.18

    Ofa Fitzgibbons
    Communication Advisor
    +61 2 4960 6188
    Ofa.Fitzgibbons@csiro.au

    Australia’s national science agency CSIRO has identified a new gene that plays a critical role in regulating the body’s immune response to infection and disease.

    1
    The C6orf106 or “C6” gene. No image credit.

    The discovery could lead to the development of new treatments for influenza, arthritis and even cancer.

    The gene, called C6orf106 or “C6”, controls the production of proteins involved in infectious diseases, cancer and diabetes. The gene has existed for 500 million years, but its potential is only now understood.

    “Our immune system produces proteins called cytokines that help fortify the immune system and work to prevent viruses and other pathogens from replicating and causing disease,” CSIRO researcher Dr Cameron Stewart said.

    “C6 regulates this process by switching off the production of certain cytokines to stop our immune response from spiralling out of control.

    “The cytokines regulated by C6 are implicated in a variety of diseases including cancer, diabetes and inflammatory disorders such as rheumatoid arthritis.”

    The discovery helps improve our understanding of our immune system, and it is hoped that this understanding will enable scientists to develop new, more targeted therapies.

    Dr Rebecca Ambrose was part of the CSIRO team that discovered the gene, and co-authored the recent paper announcing the discovery in the Journal of Biological Chemistry.

    “Even though the human genome was first fully sequenced in 2003, there are still thousands of genes that we know very little about,” Dr Rebecca Ambrose, a former CSIRO researcher, now based at the Hudson Institute of Medical Research said.

    “It’s exciting to consider that C6 has existed for more than 500 million years, preserved and passed down from simple organisms all the way to humans. But only now are we gaining insights into its importance.”

    Having discovered the function of C6, the researchers are awarded the privilege of naming it, and are enlisting the help of the community to do so.

    “The current name, C6orf106, reflects the gene’s location within the human genome, rather than relating to any particular function,” Dr Stewart said.

    “We think we can do better than that, and are inviting suggestions from the public.”

    A shortlist of names will be made available for final approval by a governing third party.

    The breakthrough builds on decades of work in infectious diseases, by researchers from CSIRO, Australia’s national science agency.

    See the full article here .


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  • richardmitnick 1:13 pm on June 18, 2018 Permalink | Reply
    Tags: DNA, , , ,   

    From Lawrence Berkeley National Lab: “Faster, Cheaper, Better: A New Way to Synthesize DNA” 

    Berkeley Logo

    From Lawrence Berkeley National Lab

    June 18, 2018
    Julie Chao
    JHChao@lbl.gov
    (510) 486-6491

    1
    Sebastian Palluk (left) and Daniel Arlow of the Joint BioEnergy Institute (JBEI) have pioneered a new way to synthesize DNA sequences. (Credit: Marilyn Chung/Berkeley Lab)

    In the rapidly growing field of synthetic biology, in which organisms can be engineered to do things like decompose plastic and manufacture biofuels and medicines, production of custom DNA sequences is a fundamental tool for scientific discovery. Yet the process of DNA synthesis, which has remained virtually unchanged for more than 40 years, can be slow and unreliable.

    Now in what could address a critical bottleneck in biology research, researchers at the Department of Energy’s Joint BioEnergy Institute (JBEI), based at Lawrence Berkeley National Laboratory (Berkeley Lab), announced they have pioneered a new way to synthesize DNA sequences through a creative use of enzymes that promises to be faster, cheaper, and more accurate. The discovery, led by JBEI graduate students Sebastian Palluk and Daniel Arlow, was published in Nature Biotechnology in a paper titled De novo DNA Synthesis Using Polymerase-Nucleotide Conjugates.

    “DNA synthesis is at the core of everything we try to do when we build biology,” said JBEI CEO Jay Keasling, the corresponding author on the paper and also a Berkeley Lab senior faculty scientist. “Sebastian and Dan have created what I think will be the best way to synthesize DNA since [Marvin] Caruthers invented solid-phase DNA synthesis almost 40 years ago. What this means for science is that we can engineer biology much less expensively – and in new ways – than we would have been able to do in the past.”

    The Caruthers process uses the tools of organic chemistry to attach DNA building blocks one at a time and has become the standard method used by DNA synthesis companies and labs around the world. However, it has drawbacks, the main ones being that it reaches its limit at about 200 bases, partly due to side reactions than can occur during the synthesis procedure, and that it produces hazardous waste. For researchers, even 1,000 bases is considered a small gene, so to make longer sequences, the shorter ones are stitched together using a process that is failure-prone and can’t make certain sequences.

    Buying your genes online

    A DNA sequence is made up of a combination of four chemical bases, represented by the letters A, C, T, and G. Researchers regularly work with genes of several thousand bases in length. To obtain them, they either need to isolate the genes from an existing organism, or they can order the genes from a company.

    “You literally paste the sequence into a website, then wait two weeks,” Arlow said. “Let’s say you buy 10 genes. Maybe nine of them will be delivered to you on time. In addition, if you want to test a thousand genes, at $300 per gene, the costs add up very quickly.”

    Palluk and Arlow were motivated to work on this problem because, as students, they were spending many long, tedious hours making DNA sequences for their experiments when they would much rather have been doing the actual experiment.

    “DNA is a huge biomolecule,” Palluk said. “Nature makes biomolecules using enzymes, and those enzymes are amazingly good at handling DNA and copying DNA. Typically our organic chemistry processes are not anywhere close to the precision that natural enzymes offer.”


    Faster, Cheaper, Better Way to Make DNA

    Thinking outside the box

    The idea of using an enzyme to make DNA is not new – scientists have been trying for decades to find a way to do it, without success. The enzyme of choice is called TdT (terminal deoxynucleotidyl transferase), which is found in the immune system of vertebrates and is one of the few enzymes in nature that writes new DNA from scratch rather than copying DNA. What’s more, it’s fast, able to add 200 bases per minute.

    In order to harness TdT to synthesize a desired sequence, the key requirement is to make it add just one nucleotide, or DNA building block, and then stop before it keeps adding the same nucleotide repeatedly. All of the previous proposals envisioned using nucleotides modified with special blocking groups to prevent multiple additions. However, the problem is that the catalytic site of the enzyme is not large enough to accept the nucleotide with a blocking group attached. “People have basically tried to ‘dig a hole’ in the enzyme by mutating it to make room for this blocking group,” Arlow said. “It’s tricky because you need to make space for it but also not screw up the activity of the enzyme.”

    Palluk and Arlow came up with a different approach. “Instead of trying to dig a hole in the enzyme, what we do is tether one nucleotide to each TdT enzyme via a cleavable linker,” Arlow said. “That way, after extending a DNA molecule using its tethered nucleotide, the enzyme has no other nucleotides available to add, so it stops. A key advantage of this approach is that the backbone of the DNA – the part that actually does the chemical reaction – is just like natural DNA, so we can try to get the full speed out of the enzyme.”

    Once the nucleotide is added to the DNA molecule, the enzyme is cleaved off. Then the cycle can begin again with the next nucleotide tethered to another TdT enzyme.

    Keasling finds the approach clever and counterintuitive. “Rather than reusing an enzyme as a catalyst, they said, ‘Hey, we can make enzymes really inexpensively. Let’s just throw it away.’ So the enzyme becomes a reagent rather than a catalyst,” he said. “That kind of thinking then allowed them to do something very different from what’s been proposed in the literature and – I think – accomplish something really important.”

    They demonstrated their method by manually making a DNA sequence of 10 bases. Not surprisingly, the two students were initially met with skepticism. “Even when we had first results, people would say, ‘It doesn’t make sense; it doesn’t seem right. That’s not how you use an enzyme,’” Palluk recalled.

    The two still have much work to do to optimize their method, but they are reasonably confident that they will be able to eventually make a gene with 1,000 bases in one go at many times the speed of the chemical method.

    Berkeley Lab has world-renowned capabilities in synthetic biology, technology development for biology, and engineering for biological process development. A number of technologies developed at JBEI and by the Lab’s Biosciences Area researchers have been spun into startups, including Lygos, Afingen, TeselaGen, and CinderBio.

    “After decades of optimization and fine-tuning, the conventional method now typically achieves a yield of about 99.5 percent per step. Our proof-of-concept synthesis had a yield of 98 percent per step, so it’s not quite on par yet, but it’s a promising starting point,” Palluk said. “We think that we’ll catch up soon and believe that we can push the system far beyond the current limitations of chemical synthesis.”

    “Our dream is to make a gene overnight,” Arlow said. “For companies trying to sustainably biomanufacture useful products, new pharmaceuticals, or tools for more environmentally friendly agriculture, and for JBEI and DOE, where we’re trying to produce fuels and chemicals from biomass, DNA synthesis is a key step. If you speed that up, it could drastically accelerate the whole process of discovery.”

    JBEI is a DOE Bioenergy Research Center funded by DOE’s Office of Science, and is dedicated to developing advanced biofuels. Other co-authors on the paper are: Tristan de Rond, Sebastian Barthel, Justine Kang, Rathin Bector, Hratch Baghdassarian, Alisa Truong, Peter Kim, Anup Singh, and Nathan Hillson.

    See the full article here .


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  • richardmitnick 2:24 pm on January 4, 2018 Permalink | Reply
    Tags: , Biocrusts, , , DNA, , LC-MS-Liquid chromatography-mass spectrometry, M. vaginatus, Metabolites, Real World Native Biocrusts: Microbial Metabolism, Soil microbiomes   

    From LBNL: “Real World Native Biocrusts: Microbial Metabolism” 

    Berkeley Logo

    Berkeley Lab

    January 4, 2018
    Dan Krotz
    dakrotz@lbl.gov

    1
    Biocrust amongst one of its many natural habitats, taken about 20 miles from the sampling site (near the Corona Arch, Moab, UT). Credit: Tami Swenson

    Arid lands, which cover some 40 percent of the Earth’s terrestrial surface, are too dry to sustain much in the way of vegetation. But far from being barren, they are home to diverse communities of microorganisms—including fungi, bacteria, and archaea—that dwell together within the uppermost millimeters of soil. These biological soil crusts, or biocrusts, can exist for extended periods in a desiccated, dormant state. When it does rain, the microbes become metabolically active, setting in motion a cascade of activity that dramatically alters both the community structure and the soil chemistry.

    “These biocrusts and other soil microbiomes contain a tremendous diversity of both microbes and small molecules (‘metabolites’). However, the connection between the chemical diversity of soil and microbial diversity is poorly understood,” said Trent Northen, a senior scientist at Lawrence Berkeley National Laboratory (Berkeley Lab).

    In a paper published January 2, 2018, in Nature Communications, Berkeley Lab researchers led by the Northen lab report that specific compounds are transformed by and strongly associated with specific bacteria in native biological soil crust (biocrust) using a suite of tools Northen calls “exometabolomics.” Understanding how microbial communities in the biocrusts adapt to their harsh environments could provide important clues to help shed light on the roles of soil microbes in the global carbon cycle.

    The work follows a 2015 study [Nature Communications] that examined how specific small molecule compounds called “metabolites” were transformed in a mixture of bacterial isolates from biocrust samples cultured in a milieu of metabolites from the same soil. “We found that the microbes we investigated were ‘picky’ eaters,” Northen said. “We thought we could use this information to link what’s being consumed to the abundance of the microbes in the intact community, thereby linking the biology to the chemistry.”

    In the new study, the investigators set out to determine whether the microbe-metabolite relationships observed in the simplified test-tube system could be reproduced in a more complex soil environment.

    Biocrusts from the same source – representing four successive stages of maturation – were wet, and the soil water was sampled at five time points. The samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to characterize the metabolite composition (“metabolomics”), and biocrust DNA was extracted for shotgun sequencing to measure single copy gene markers for the dominant microbe species (“metagenomics”).

    4
    Biocrust is held together primarily by exopolysaccharides produced by the filamentous Cyanobacterium, M. vaginatus. Samples from the field were collected in petri dishes. In the lab, they were removed from the dishes, cut and placed into multi-well plates before adding water. Credit: Tami Swenson.

    “When we compare the patterns of metabolite uptake and production for isolated bacteria that are related to the most abundant microbes found in the biocrusts, we find that, excitingly, these patterns are maintained,” said Northen. That is, increased abundance of a given microbe is negatively correlated with the metabolites that they consume and positively correlated with metabolites that they release.

    When active, biocrusts take up atmospheric carbon dioxide and fix nitrogen, contributing to the ecosystem’s primary productivity. They also process organic matter in soil, modifying key properties related to soil fertility and water availability.

    “This study suggests that laboratory studies of microbial metabolite processing can help understand the role of these microbes in carbon cycling in the environment. This study gets us closer to understanding the complex food webs that are vital in nutrient dynamics and overall soil fertility,” said study first author Tami Swenson, a scientific engineering associate in Northen’s group within the Berkeley Lab Biosciences Area’s Environmental Genomics and Systems Biology (EGSB) Division.

    Northen’s group is currently working on expanding these studies to capture a greater fraction of microbial diversity. Ultimately, this may enable the prediction of nutrient cycling in terrestrial microbial ecosystems, and perhaps even manipulation by adding specific metabolites.

    The following Berkeley Lab researchers also contributed to the study: Benjamin Bowen, a member of Northen’s lab in EGSB and at the Joint Genome Institute, a DOE Office of Science User Facility, helped analyze metabolomics data; Ulas Karaoz in the Earth and Environmental Sciences Area (EESA) analyzed metagenomics data; and Joel Swenson, a former postdoctoral researcher in Biosciences’ Biological Systems and Engineering Division, helped conduct correlation and statistical analyses.

    This work was supported under a DOE Office of Science Early Career Research Program award. DNA was sequenced using the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by a National Institutes of Health Instrumentation Grant.

    5
    Regular water was added to mimic a rainfall event. The microbes in biocrust become metabolically active immediately upon wetting. As seen here, M. vaginatus turns green and releases oxygen. Credit: Tami Swenson.

    See the full article here .

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  • richardmitnick 8:05 pm on October 15, 2017 Permalink | Reply
    Tags: , , , DNA, , , Nanotechnology is a multidisciplinary field where chemistry medicine and engineering all intersect, , , Spherical nucleic acid (SNA) technology, Studying and manipulating molecules and materials with dimensions on the 1 to 100 nanometer length scale (1 nm = one billionth of a meter)   

    From Northwestern University- “Titans of nanotechnology: The next big thing is very small” 

    Northwestern U bloc
    Northwestern University

    October 09, 2017

    1
    Teri Odom and Chad Mirkin of the International Institute for Nanotechnology.

    World-renowned nanoscientists and chemists Chad Mirkin, the Director of the International Institute for Nanotechnology (IIN) at Northwestern University, and Teri Odom, the IIN’s Associate Director, sit down to discuss the golden age of miniaturization and how the “science of small things” is fostering major advances.

    The IIN, founded in 2000, is making major strides in nanotechnology and thriving in a big way. Nanoscience and technology — a field focused on studying and manipulating molecules and materials with dimensions on the 1 to 100 nanometer length scale (1 nm = one billionth of a meter) — was anticipated in 1959 by physicist Richard Feynman and made possible with the advent of the electron and scanning tunneling microscopes in the 1980s. It is engaging scientists from all over the world across many disciplines. They are using such tools to explore, and ultimately solve, some of the world’s most pressing issues in medicine, engineering, energy, and defense.

    We [interviewer is not named] sit in on a conversation between Mirkin and Odom to see where this exciting field is headed.

    Q: Your team discovered spherical nucleic acid (SNA) technology, where tiny particles can be decorated with short snippets of DNA or RNA. With the creation of SNAs, you’ve basically taken known molecules, reorganized them at the nanoscale into ball-like forms, and changed their properties. What is the potential of such a discovery, and what exciting breakthroughs are on the near horizon?

    Mirkin: Two really promising areas in which we are applying SNA technology are biomedicine and gene regulation — the idea that one can create ways of using DNA- and RNA-based SNAs as potent new drugs. For example, we can put SNAs into commercially available creams, like Aquaphor®, and apply them topically to treat diseases of the skin. There are more than 200 skin diseases with a known genetic basis, making the DNA- and RNA-based SNAs a general strategy for treating skin diseases. Conventional DNA and RNA constructs based on linear nucleic acids cannot be delivered in this way – they do not penetrate the skin. But, SNAs can because of their unique architecture that changes the way they interact with biological structures and in particular, receptors on skin cells that recognize them, but not linear DNA or RNA. SNAs can also be used to treat diseases of the bladder, colon, lung, and eye — organs and tissues that also are hard to treat using traditional means.

    Q: Nanotechnology is a multidisciplinary field where chemistry, medicine and engineering all intersect to create innovative solutions for a whole range of issues. One area is photonics, where advances at the nanoscale are changing how we communicate. How?

    Odom: We’re trying to reduce the size of lasers, which are typically macroscopic devices, down to the nanometer scale. The ability to design nanomaterials that can control the production and guiding of light — which is composed of individual particles called photons — can transform a range of different technologies. For example, communication based on photons (like in optical fibers) vs. electrons (like in copper wires) is faster and much more efficient. Applications that exploit light can readily be transformed by nanotechnology.

    Q: Nanotechnology has revolutionized the basic sciences, fast-tracking their translational impact. For example, your colleague Samuel Stupp, director of the Simpson Querrey Institute for BioNanotechnology at Northwestern, is on the verge of conducting clinical trials in spinal regeneration through “soft” nanotechnology breakthroughs. Has nanotechnology also revolutionized the traditional scientific method, too?

    Mirkin: The desire to come up with a solution to a given problem often leads scientists to develop new capabilities. That’s the thrilling thing about science in general, but about nanotechnology in particular: we often have goals, which are driven by engineering needs, but along the way we discover fundamentally interesting principles that we didn’t anticipate and that inform our view of the world around us. These discoveries take us down new paths — ones that might be even more interesting than the original ones we were on. This is the nature and importance of basic science research.

    Odom: Nano provides the fundamentals. But then, we adapt, based on these unanticipated properties, while still keeping our long-range goals in mind. That’s pretty neat. You can adjust in ways that keep discovery and creativity at the forefront. Without that, we all would be bored.

    Q: Nobel Prize winner Sir Fraser Stoddart, John Rogers, William Dichtel, Milan Mrksich and the aforementioned Stupp are just a few of the many big names in the Northwestern nanotechnology community. What is Northwestern doing right and what’s the global impact?

    Mirkin: These are heavy hitters, people who can go anywhere in the world, but they chose to come to Northwestern because they recognized that this is a very special time in our history. We are on an incredible trajectory here, and they want to be a part of it.

    Odom: We have a holistic way of training new faculty and graduate students because we want them to have a complete picture of everything that’s going on here. This is how we do science at Northwestern, and we really apply it to nanotechnology. Part of our success as a chemistry department has come from our ability to make things, to measure them, and to model them — I like to think of this integration as the “3Ms” principle. Our achievements in nanotechnology have been built on these three synergistic areas of expertise.

    Mirkin: It really starts with world-class talent, and then collaboration. You can collaborate all you want, but if you don’t have world-class talent, it doesn’t matter. Since we’re going all-in on the medical side, in 15 years I went from having zero collaborations with the medical school, to now having 17. There is a natural interaction here between clinicians, scientists, and engineers that make everyone’s work so much stronger. Within the next five years, I anticipate that there will be cancer treatments based upon nanotechnology that greatly improve outcomes and, in some subsets of diseases, actually leads to cures.

    See the full article here .

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    On May 31, 1850, nine men gathered to begin planning a university that would serve the Northwest Territory.

    Given that they had little money, no land and limited higher education experience, their vision was ambitious. But through a combination of creative financing, shrewd politicking, religious inspiration and an abundance of hard work, the founders of Northwestern University were able to make that dream a reality.

    In 1853, the founders purchased a 379-acre tract of land on the shore of Lake Michigan 12 miles north of Chicago. They established a campus and developed the land near it, naming the surrounding town Evanston in honor of one of the University’s founders, John Evans. After completing its first building in 1855, Northwestern began classes that fall with two faculty members and 10 students.
    Twenty-one presidents have presided over Northwestern in the years since. The University has grown to include 12 schools and colleges, with additional campuses in Chicago and Doha, Qatar.

    Northwestern is recognized nationally and internationally for its educational programs.

     
  • richardmitnick 1:19 pm on September 13, 2017 Permalink | Reply
    Tags: , , DNA, , , PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography), , TFIIH-Transcription factor IIH   

    From LBNL: “Berkeley Lab Scientists Map Key DNA Protein Complex at Near-Atomic Resolution” 

    Berkeley Logo

    Berkeley Lab

    September 13, 2017
    Sarah Yang
    scyang@lbl.gov
    (510) 486-4575

    1
    The cryo-EM structure of Transcription Factor II Human (TFIIH). The atomic coordinate model, colored according to the different TFIIH subunits, is shown inside the semi-transparent cryo-EM map. (Credit: Basil Greber/Berkeley Lab and UC Berkeley)

    Chalking up another success for a new imaging technology that has energized the field of structural biology, researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) obtained the highest resolution map yet of a large assembly of human proteins that is critical to DNA function.

    The scientists are reporting their achievement today in an advanced online publication of the journal Nature. They used cryo-electron microscopy (cryo-EM) to resolve the 3-D structure of a protein complex called transcription factor IIH (TFIIH) at 4.4 angstroms, or near-atomic resolution. This protein complex is used to unzip the DNA double helix so that genes can be accessed and read during transcription or repair.

    “When TFIIH goes wrong, DNA repair can’t occur, and that malfunction is associated with severe cancer propensity, premature aging, and a variety of other defects,” said study principal investigator Eva Nogales, faculty scientist at Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging Division. “Using this structure, we can now begin to place mutations in context to better understand why they give rise to misbehavior in cells.”

    TFIIH’s critical role in DNA function has made it a prime target for research, but it is considered a difficult protein complex to study, especially in humans.

    ___________________________________________________________________
    How to Capture a Protein
    1
    It takes a large store of patience and persistence to prepare specimens of human transcription factor IIH (TFIIH) for cryo-EM. Because TFIIH exists in such minute amounts in a cell, the researchers had to grow 50 liters of human cells in culture to yield a few micrograms of the purified protein.

    Human TFIIH is particularly fragile and prone to falling apart in the flash-freezing process, so researchers need to use an optimized buffer solution to help protect the protein structure.

    “These compounds that protect the proteins also work as antifreeze agents, but there’s a trade-off between protein stability and the ability to produce a transparent film of ice needed for cryo-EM,” said study lead author Basil Greber.

    Once Greber obtains a usable sample, he settles down for several days at the cryo-electron microscope at UC Berkeley’s Stanley Hall for imaging.

    “Once you have that sample inside the microscope, you keep collecting data as long as you can,” he said. “The process can take four days straight.”
    ___________________________________________________________________

    Mapping complex proteins

    “As organisms get more complex, these proteins do, too, taking on extra bits and pieces needed for regulatory functions at many different levels,” said Eva Nogales, who is also a UC Berkeley professor of molecular and cell biology and a Howard Hughes Medical Institute investigator. “The fact that we resolved this protein structure from human cells makes this even more relevant to disease research. There’s no need to extrapolate the protein’s function based upon how it works in other organisms.”

    Biomolecules such as proteins are typically imaged using X-ray crystallography, but that method requires a large amount of stable sample for the crystallization process to work. The challenge with TFIIH is that it is hard to produce and purify in large quantities, and once obtained, it may not form crystals suitable for X-ray diffraction.

    Enter cryo-EM, which can work even when sample amounts are very small. Electrons are sent through purified samples that have been flash-frozen at ultracold temperatures to prevent crystalline ice from forming.

    Cryo-EM has been around for decades, but major advances over the past five years have led to a quantum leap in the quality of high-resolution images achievable with this technique.

    “When your goal is to get resolutions down to a few angstroms, the problem is that any motion gets magnified,” said study lead author Basil Greber, a UC Berkeley postdoctoral fellow at the California Institute for Quantitative Biosciences (QB3). “At high magnifications, the slight movement of the specimen as electrons move through leads to a blurred image.”

    Making movies

    The researchers credit the explosive growth in cryo-EM to advanced detector technology that Berkeley Lab engineer Peter Denes helped develop. Instead of a single picture taken for each sample, the direct detector camera shoots multiple frames in a process akin to recording a movie. The frames are then put together to create a high-resolution image. This approach resolves the blur from sample movement. The improved images contain higher quality data, and they allow researchers to study the sample in multiple states, as they exist in the cell.

    Since shooting a movie generates far more data than a single frame, and thousands of movies are being collected during a microscopy session, the researchers needed the processing punch of supercomputers at the National Energy Research Scientific Computing Center (NERSC) at Berkeley Lab.

    NERSC Cray Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer

    NERSC Hopper Cray XE6 supercomputer

    The output from these computations was a 3-D map that required further interpretation.

    “When we began the data processing, we had 1.5 million images of individual molecules to sort through,” said Greber. “We needed to select particles that are representative of an intact complex. After 300,000 CPU hours at NERSC, we ended up with 120,000 images of individual particles that were used to compute the 3-D map of the protein.”

    To obtain an atomic model of the protein complex based on this 3-D map, the researchers used PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography), a software program whose development is led by Paul Adams, director of Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging Division and a co-author of this study.

    Not only does this structure improve basic understanding of DNA repair, the information could be used to help visualize how specific molecules are binding to target proteins in drug development.

    “In studying the physics and chemistry of these biological molecules, we’re often able to determine what they do, but how they do it is unclear,” said Nogales. “This work is a prime example of what structural biologists do. We establish the framework for understanding how the molecules function. And with that information, researchers can develop finely targeted therapies with more predictive power.”

    Other co-authors on this study are Pavel Afonine and Thi Hoang Duong Nguyen, both of whom have joint appointments at Berkeley Lab and UC Berkeley; and Jie Fang, a researcher at the Howard Hughes Medical Institute.

    NERSC is a DOE Office of Science User Facility located at Berkeley Lab. In addition to NERSC, the researchers used the Lawrencium computing cluster at Berkeley Lab. This work was funded by the National Institute of General Medical Sciences and the Swiss National Science Foundation.

    See the full article here .

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  • richardmitnick 9:41 am on August 14, 2017 Permalink | Reply
    Tags: Acidic patch, Acidic patch’ regulates access to genetic information, , , , Chromatin remodelers, DNA, , ISWI remodelers,   

    From Princeton: “‘Acidic patch’ regulates access to genetic information” 

    Princeton University
    Princeton University Research Blog

    August 14, 2017
    Pooja Makhijani

    Chromatin remodelers — protein machines that pack and unpack chromatin, the tightly wound DNA-protein complex in cell nuclei — are essential and powerful regulators for critical cellular processes, such as replication, recombination and gene transcription and repression. In a new study published Aug. 2 in the journal Nature, a team led by researchers from Princeton University unravels more details on how a class of ATP-dependent chromatin remodelers, called ISWI, regulate access to genetic information.

    The researchers reported that ISWI remodelers use a structural feature of the nucleosome, known as the “acidic patch,” to remodel chromatin. The nucleosome is the fundamental structural subunit of chromatin, and is often compared to thread wrapped around a spool.

    “The acidic patch is a negatively charged surface, presented on each face of the nucleosome disc, that is formed by amino acids contributed by two different histone proteins, H2A and H2B,” said Geoffrey Dann, a graduate student in the Department of Molecular Biology at Princeton and the study’s lead author. “Histone proteins are overall very positively charged, which makes the negatively charged acidic patch region of the nucleosome very unique. Recognition of the acidic patch has never before been implicated in chromatin remodeling.”

    The research was conducted in the laboratory of Tom Muir, the Van Zandt Williams Jr. Class of 1965 Professor of Chemistry and chair of the Department of Chemistry. Research in the Muir group centers on elucidating the physiochemical basis of protein functions in biomedically relevant systems.

    Because ISWI remodelers are known to interact extensively with nucleosomes, the researchers hypothesized that signals, in the form of chemical modifications on histone proteins embedded within nucleosomes, communicate to the remodelers on which nucleosome to act. Using high throughput screening technology, an assay process often used in drug discovery, allowed the researchers to quickly conduct tens of thousands of biochemical measurements to test their assumptions. “The number of chromatin modifications known to exist in vivo is astronomical,” Dann said.

    Not only did the experiments reveal that ISWI remodelers use the “acidic patch” to remodel chromatin, but also determined that remodeling enzymes outside the family of ISWI remodelers also use this structural feature, “suggesting that this feature may be a general requirement for chromatin remodeling to occur,” Dann said.

    1
    Geoffrey Dann. Photo by Jeffrey Bos.

    Certain chemical modifications that act on histone proteins that are adjacent to the acidic patch also have the ability to enhance or inhibit ISWI remodeling activity, he explained. “A handful of other proteins are known to engage the acidic patch in their interaction with chromatin as well, and we also found that the biochemistry of several of these proteins was affected by such modifications. Interestingly, each protein tested had its own signature response to this collection of modifications.”

    The high throughput screening technology method also generated a vast library of data to drive the design of future studies geared toward further understanding ISWI regulation. “This study generated an immense amount of data pointing to many other novel regulatory inputs, in the form of chromatin modifications, into ISWI remodeling activity,” Dann said. “A long-term goal in our lab is to use this data resource as a launch pad for additional studies investigating how chromatin modifications affect ISWI remodeling, and how this plays into the various roles ISWI remodelers assume in the cell.”

    Their findings may also identify a new instrument in cells’ molecular repertoire of chromatin-remodeling tools and spur investigations into potential cancer therapeutic targets. “Mutations in the acidic patch are known to occur in certain types of human cancers, which underscores the emerging importance of the acidic patch in chromatin biology,” Dann said.

    See the full article here .

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    Princeton University Campus

    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

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  • richardmitnick 11:53 am on July 29, 2017 Permalink | Reply
    Tags: 3D structure of human chromatin, , ChromEMT, DNA, , , , ,   

    From Salk: “Salk scientists solve longstanding biological mystery of DNA organization” 

    Salk Institute bloc

    Salk Institute for Biological Studies

    July 27, 2017

    Stretched out, the DNA from all the cells in our body would reach Pluto. So how does each tiny cell pack a two-meter length of DNA into its nucleus, which is just one-thousandth of a millimeter across?

    The answer to this daunting biological riddle is central to understanding how the three-dimensional organization of DNA in the nucleus influences our biology, from how our genome orchestrates our cellular activity to how genes are passed from parents to children.

    Now, scientists at the Salk Institute and the University of California, San Diego, have for the first time provided an unprecedented view of the 3D structure of human chromatin—the combination of DNA and proteins—in the nucleus of living human cells.

    In the tour de force study, described in Science on July 27, 2017, the Salk researchers identified a novel DNA dye that, when paired with advanced microscopy in a combined technology called ChromEMT, allows highly detailed visualization of chromatin structure in cells in the resting and mitotic (dividing) stages. By revealing nuclear chromatin structure in living cells, the work may help rewrite the textbook model of DNA organization and even change how we approach treatments for disease.

    “One of the most intractable challenges in biology is to discover the higher-order structure of DNA in the nucleus and how is this linked to its functions in the genome,” says Salk Associate Professor Clodagh O’Shea, a Howard Hughes Medical Institute Faculty Scholar and senior author of the paper. “It is of eminent importance, for this is the biologically relevant structure of DNA that determines both gene function and activity.”

    2
    A new technique enables 3D visualization of chromatin (DNA plus associated proteins) structure and organization within a cell nucleus (purple, bottom left) by painting the chromatin with a metal cast and imaging it with electron microscopy (EM). The middle block shows the captured EM image data, the front block illustrates the chromatin organization from the EM data, and the rear block shows the contour lines of chromatin density from sparse (cyan and green) to dense (orange and red). Credit: Salk Institute.

    Ever since Francis Crick and James Watson determined the primary structure of DNA to be a double helix, scientists have wondered how DNA is further organized to allow its entire length to pack into the nucleus such that the cell’s copying machinery can access it at different points in the cell’s cycle of activity. X-rays and microscopy showed that the primary level of chromatin organization involves 147 bases of DNA spooling around proteins to form particles approximately 11 nanometers (nm) in diameter called nucleosomes. These nucleosome “beads on a string” are then thought to fold into discrete fibers of increasing diameter (30, 120, 320 nm etc.), until they form chromosomes. The problem is, no one has seen chromatin in these discrete intermediate sizes in cells that have not been broken apart and had their DNA harshly processed, so the textbook model of chromatin’s hierarchical higher-order organization in intact cells has remained unverified.

    To overcome the problem of visualizing chromatin in an intact nucleus, O’Shea’s team screened a number of candidate dyes, eventually finding one that could be precisely manipulated with light to undergo a complex series of chemical reactions that would essentially “paint” the surface of DNA with a metal so that its local structure and 3D polymer organization could be imaged in a living cell. The team partnered with UC San Diego professor and microscopy expert Mark Ellisman, one of the paper’s coauthors, to exploit an advanced form of electron microscopy that tilts samples in an electron beam enabling their 3D structure to be reconstructed. By combining their chromatin dye with electron-microscope tomography, they created ChromEMT.

    The team used ChromEMT to image and measure chromatin in resting human cells and during cell division when DNA is compacted into its most dense form—the 23 pairs of mitotic chromosomes that are the iconic image of the human genome. Surprisingly, they did not see any of the higher-order structures of the textbook model anywhere.

    3
    From left: Horng Ou and Clodagh O’Shea. Credit: Salk Institute.

    “The textbook model is a cartoon illustration for a reason,” says Horng Ou, a Salk research associate and the paper’s first author. “Chromatin that has been extracted from the nucleus and subjected to processing in vitro—in test tubes—may not look like chromatin in an intact cell, so it is tremendously important to be able to see it in vivo.”

    What O’Shea’s team saw, in both resting and dividing cells, was chromatin whose “beads on a string” did not form any higher-order structure like the theorized 30 or 120 or 320 nanometers. Instead, it formed a semi-flexible chain, which they painstakingly measured as varying continuously along its length between just 5 and 24 nanometers, bending and flexing to achieve different levels of compaction. This suggests that it is chromatin’s packing density, and not some higher-order structure, that determines which areas of the genome are active and which are suppressed.

    With their 3D microscopy reconstructions, the team was able to move through a 250 nm x 1000 nm x 1000 nm volume of chromatin’s twists and turns, and envision how a large molecule like RNA polymerase, which transcribes (copies) DNA, might be directed by chromatin’s variable packing density, like a video game aircraft flying through a series of canyons, to a particular spot in the genome. Besides potentially upending the textbook model of DNA organization, the team’s results suggest that controlling access to chromatin could be a useful approach to preventing, diagnosing and treating diseases such as cancer.

    “We show that chromatin does not need to form discrete higher-order structures to fit in the nucleus,” adds O’Shea. “It’s the packing density that could change and limit the accessibility of chromatin, providing a local and global structural basis through which different combinations of DNA sequences, nucleosome variations and modifications could be integrated in the nucleus to exquisitely fine-tune the functional activity and accessibility of our genomes.”

    Future work will examine whether chromatin’s structure is universal among cell types or even among organisms.

    Other authors included Sébastien Phan, Thomas Deerinck and Andrea Thor of the UC San Diego.

    The work was largely funded by the W. M. Keck Foundation, the NIH 4D Nucleome Roadmap Initiative and the Howard Hughes Medical Institute, with additional support from the William Scandling Trust, the Price Family Foundation and the Leona M. and Harry B. Helmsley Charitable Trust.

    See the full article here .

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    Salk Institute Campus

    Every cure has a starting point. Like Dr. Jonas Salk when he conquered polio, Salk scientists are dedicated to innovative biological research. Exploring the molecular basis of diseases makes curing them more likely. In an outstanding and unique environment we gather the foremost scientific minds in the world and give them the freedom to work collaboratively and think creatively. For over 50 years this wide-ranging scientific inquiry has yielded life-changing discoveries impacting human health. We are home to Nobel Laureates and members of the National Academy of Sciences who train and mentor the next generation of international scientists. We lead biological research. We prize discovery. Salk is where cures begin.

     
  • richardmitnick 3:16 pm on July 17, 2017 Permalink | Reply
    Tags: A key building block for controlling microbiomes, Controlling gene expression across bacterial colonies, DNA, , Master clock, Programming the clock, ,   

    From UCSD Jacobs School of Engineering: “Scientists at the UC San Diego Center for Microbiome Innovation invent new tool for the Synthetic Biologist’s toolbox” 

    UC San Diego bloc

    UC San Diego


    Jacobs School of Engineering

    July 10, 2017
    Mario Aguilera
    Scripps Institute of Oceanography
    Phone: 858-534-3624
    scrippsnews@ucsd.edu

    Researchers at the University of California San Diego have invented a new method for controlling gene expression across bacterial colonies. The method involves engineering dynamic DNA copy number changes in a synchronized fashion. The results were published in the July 10, 2017 online edition of Nature Genetics.

    Until now, methods for controlling or programming bacterial cells involved transcriptional and post-transcriptional regulation. UC San Diego researchers led by Jeff Hasty, a professor of bioengineering and biology and member of the UC San Diego Center for Microbiome Innovation, describe a new method, which involves cutting circular pieces of bacterial DNA called plasmids, effectively destroying the DNA and turning off regulation.

    The study also demonstrates how DNA concentration can be increased to turn on a synthetic gene circuit. By controlling DNA copy number, researchers can effectively regulate gene expression.

    Synthetic Biology – which can involve altering biological systems for some purpose – is emerging as an engineering discipline. The field was firmly established in 2000, with the description of synthetic biological circuits in which parts of a cell are designed to perform functions, similar to the way an electronic circuit works. Also similar to an electronic circuit, the task performed by a biological circuit can be turned on and off. At the same time, researchers described the making of a “genetic clock”, which involves placing genes in a particular order so that they’ll be turned on at a specific time. This approach has also helped researchers understand natural “oscillators”, such as our sleep-wake cycle.

    Since these early inventions, Hasty and his team have shown how engineered cellular oscillations can be synchronized within a bacterial colony using plasmids, synthetically designed by the researchers themselves. Now, the team is adding a new tool to the Synthetic Biologist’s toolbox – a “master clock” of sorts that will allow researchers to coordinate subprocesses in bacterial cells.

    “This remarkable achievement is a key building block for controlling microbiomes”, said Rob Knight, professor of pediatrics at UC San Diego with a joint appointment in computer science and engineering. Knight leads the Center for Microbiome Innovation. “By controlling different strains with the same master clock, or by giving different strains their own clocks, we can start to engineer population-level dynamics to control specific microbiome functions.”

    Examples of these functions might include interaction with host cells at particular times of day, such as timed release of neurotransmitters produced by the bacteria, or interactions with other bacteria such as antifungal production triggered by a meal rich in sugar.

    Programming the clock

    The researchers used an endonuclease from Saccharomyces cerevisiae, a species of yeast, expressed alongside a plasmid containing the nuclease recognition sequence to temporarily reduce the plasmid’s copy number below natural levels.

    “We found that plasmid replication is so strong that we couldn’t cut them all,” said Hasty. “This was good news, because it meant we could down-regulate gene expression, but not eliminate it.”

    The researchers reasoned that the method could be used to regulate an entire suite of genes and promoters, and tested their idea using a previously constructed circuit to produce sustained cycling of DNA plasmid concentration across a colony of E. coli cells.

    The circuit works by using a small molecule, known as AHL, to coordinate gene expression across a colony of bacterial cells. Once on, the genes driven by the promoter are also activated, including the AHL-producing gene itself. Thanks to this positive feedback loop, the more AHL accumulates, the more it is produced. Because AHL is small enough to diffuse between cells and turn on the promoter in neighboring cells, the genes activated by it would also be produced in high amounts, leading to a phenomenon known as quorum sensing.

    Hasty and his team employed the endonuclease to reduce the number of these plasmids present in the colony and used this mechanism as negative feedback to driving the oscillations in gene expression. Using quorum sensing, the feedback system was coupled across the colony of cells.

    “We observed regular oscillations of gene expression in microfluidic chambers at different colony length scales and over extended time periods,” said Hasty. “By incorporating elements for both positive and negative copy number regulation, we were able to improve the robustness of the circuit.”

    See the full article here .

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    UC San Diego Campus

    About the Jacobs School
    Innovation Happens Here

    The UC San Diego Jacobs School of Engineering is a premier research school set apart by our entrepreneurial culture and integrative engineering approach.

    The Jacobs School’s Mission:

    Educate Tomorrow’s Technology Leaders
    Conduct Leading Edge Research and Drive Innovation
    Transfer Discoveries for the Benefit of Society

    The Jacobs School’s Values:

    Engineering for the global good
    Exponential impact through entrepreneurism
    Collaboration to enrich relevance
    Our education models focus on deep and broad engineering fundamentals, enhanced by real-world design and research, often in partnership with industry. Through our Team Internship Program and GlobalTeams in Engineering Service program, for example, we encourage students to develop their communications and leadership skills while working in the kind of multi-disciplinary team environment experienced by real-world engineers.

    We are home to exciting research centers, such as the San Diego Supercomputer Center, a national resource for data-intensive computing; our Powell Structural Research Laboratories, the largest and most active in the world for full-scale structural testing; and the Qualcomm Institute, which is the UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2), which is forging new ground in multi-disciplinary applications for information technology.

    Located at the hub of San Diego’s thriving information technology, biotechnology, clean technology, and nanotechnology sectors, the Jacobs School proactively seeks corporate partners to collaborate with us in research, education and innovation.

    The University of California, San Diego (also referred to as UC San Diego or UCSD), is a public research university located in the La Jolla area of San Diego, California, in the United States.[12] The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha).[13] Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. UC San Diego is one of America’s Public Ivy universities, which recognizes top public research universities in the United States. UC San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report ‘s 2015 rankings.

     
  • richardmitnick 8:47 am on July 17, 2017 Permalink | Reply
    Tags: , CRISPR-Cas3, DNA, , , ,   

    From HMS: “Bringing CRISPR into Focus” 

    Harvard University

    Harvard University

    Harvard Medical School

    Harvard Medical School

    June 29, 2017
    KEVIN JIANG

    CRISPR-Cas3 is a subtype of the CRISPR-Cas system, a widely adopted molecular tool for precision gene editing in biomedical research. Aspects of its mechanism of action, however, particularly how it searches for its DNA targets, were unclear, and concerns about unintended off-target effects have raised questions about the safety of CRISPR-Cas for treating human diseases.

    Harvard Medical School and Cornell University scientists have now generated near-atomic resolution snapshots of CRISPR that reveal key steps in its mechanism of action. The findings, published in Cell on June 29, provide the structural data necessary for efforts to improve the efficiency and accuracy of CRISPR for biomedical applications.

    Through cryo-electron microscopy, the researchers describe for the first time the exact chain of events as the CRISPR complex loads target DNA and prepares it for cutting by the Cas3 enzyme. These structures reveal a process with multiple layers of error detection—a molecular redundancy that prevents unintended genomic damage, the researchers say.

    High-resolution details of these structures shed light on ways to ensure accuracy and avert off-target effects when using CRISPR for gene editing.

    “To solve problems of specificity, we need to understand every step of CRISPR complex formation,” said Maofu Liao, assistant professor of cell biology at Harvard Medical School and co-senior author of the study. “Our study now shows the precise mechanism for how invading DNA is captured by CRISPR, from initial recognition of target DNA and through a process of conformational changes that make DNA accessible for final cleavage by Cas3.”

    Target search

    Discovered less than a decade ago, CRISPR-Cas is an adaptive defense mechanism that bacteria use to fend off viral invaders. This process involves bacteria capturing snippets of viral DNA, which are then integrated into its genome and which produce short RNA sequences known as crRNA (CRISPR RNA). These crRNA snippets are used to spot “enemy” presence.

    Acting like a barcode, crRNA is loaded onto members of the CRISPR family of enzymes, which perform the function of sentries that roam the bacteria and monitor for foreign code. If these riboprotein complexes encounter genetic material that matches its crRNA, they chop up that DNA to render it harmless. CRISPR-Cas subtypes, notably Cas9, can be programmed with synthetic RNA in order to cut genomes at precise locations, allowing researchers to edit genes with unprecedented ease.

    To better understand how CRISPR-Cas functions, Liao partnered with Ailong Ke of Cornell University. Their teams focused on type 1 CRISPR, the most common subtype in bacteria, which utilizes a riboprotein complex known as CRISPR Cascade for DNA capture and the enzyme Cas3 for cutting foreign DNA.

    Through a combination of biochemical techniques and cryo-electron microscopy, they reconstituted stable Cascade in different functional states, and further generated snapshots of Cascade as it captured and processed DNA at a resolution of up to 3.3 angstroms—or roughly three times the diameter of a carbon atom.

    1
    A sample cryo-electron microscope image of CRISPR molecules(left). The research team combined hundreds of thousands of particles into 2D averages (right), before turning them into 3D projections. Image: Xiao et al.

    Seeing is believing

    In CRISPR-Cas3, crRNA is loaded onto CRISPR Cascade, which searches for a very short DNA sequence known as PAM that indicates the presence of foreign viral DNA.

    Liao, Ke and their colleagues discovered that as Cascade detects PAM, it bends DNA at a sharp angle, forcing a small portion of the DNA to unwind. This allows an 11-nucleotide stretch of crRNA to bind with one strand of target DNA, forming a “seed bubble.”

    The seed bubble acts as a fail-safe mechanism to check whether the target DNA matches the crRNA. If they match correctly, the bubble is enlarged and the remainder of the crRNA binds with its corresponding target DNA, forming what is known as an “R-loop” structure.

    Once the R-loop is completely formed, the CRISPR Cascade complex undergoes a conformational change that locks the DNA into place. It also creates a bulge in the second, non-target strand of DNA, which is run through a separate location on the Cascade complex.

    Only when a full R-loop state is formed does the Cas3 enzyme bind and cut the DNA at the bulge created in the non-target DNA strand.

    The findings reveal an elaborate redundancy to ensure precision and avoid mistakenly chopping up the bacteria’s own DNA.

    2
    CRISPR forms a “seed bubble” state, which acts as an initial fail-safe mechanism to ensure that CRISPR RNA matches its target DNA. Image: Liao Lab/HMS.

    “To apply CRISPR in human medicine, we must be sure the system is accurate and that it does not target the wrong genes,” said Ke, who is co-senior author of the study. “Our argument is that the CRISPR-Cas3 subtype has evolved to be a precise system that carries the potential to be a more accurate system to use for gene editing. If there is mistargeting, we know how to manipulate the system because we know the steps involved and where we might need to intervene.”

    Setting the sights

    Structures of CRISPR Cascade without target DNA and in its post-R-loop conformational states have been described, but this study is the first to reveal the full sequence of events from seed bubble formation to R-loop formation at high resolution.

    In contrast to the scalpel-like Cas9, CRISPR-Cas3 acts like a shredder that chews DNA up beyond repair. While CRISPR-Cas3 has, thus far, limited utility for precision gene editing, it is being developed as a tool to combat antibiotic-resistant strains of bacteria. A better understanding of its mechanisms may broaden the range of potential applications for CRISPR-Cas3.

    In addition, all CRISPR-Cas subtypes utilize some version of an R-loop formation to detect and prepare target DNA for cleavage. The improved structural understanding of this process can now enable researchers to work toward modifying multiple types of CRISPR-Cas systems to improve their accuracy and reduce the chance of off-target effects in biomedical applications.

    “Scientists hypothesized that these states existed but they were lacking the visual proof of their existence,” said co-first author Min Luo, postdoctoral fellow in the Liao lab at HMS. “The main obstacles came from stable biochemical reconstitution of these states and high-resolution structural visualization. Now, seeing really is believing.”

    “We’ve found that these steps must occur in a precise order,” Luo said. “Evolutionarily, this mechanism is very stringent and has triple redundancy, to ensure that this complex degrades only invading DNA.”

    Additional authors on the study include Yibei Xiao, Robert P. Hayes, Jonathan Kim, Sherwin Ng, and Fang Ding.

    This work is supported by National Institutes of Health grants GM 118174 and GM102543.

    See the full article here .

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    HMS campus

    Established in 1782, Harvard Medical School began with a handful of students and a faculty of three. The first classes were held in Harvard Hall in Cambridge, long before the school’s iconic quadrangle was built in Boston. With each passing decade, the school’s faculty and trainees amassed knowledge and influence, shaping medicine in the United States and beyond. Some community members—and their accomplishments—have assumed the status of legend. We invite you to access the following resources to explore Harvard Medical School’s rich history.

    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 1:21 pm on July 8, 2017 Permalink | Reply
    Tags: , , , , DNA, , , , , UCSD Comet supercomputer   

    From Science Node: “Cracking the CRISPR clock” 

    Science Node bloc
    Science Node

    05 Jul, 2017
    Jan Zverina

    SDSC Dell Comet supercomputer

    Capturing the motion of gyrating proteins at time intervals up to one thousand times greater than previous efforts, a team led by University of California, San Diego (UCSD) researchers has identified the myriad structural changes that activate and drive CRISPR-Cas9, the innovative gene-splicing technology that’s transforming the field of genetic engineering.

    By shedding light on the biophysical details governing the mechanics of CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) activity, the study provides a fundamental framework for designing a more efficient and accurate genome-splicing technology that doesn’t yield ‘off-target’ DNA breaks currently frustrating the potential of the CRISPR-Cas9- system, particularly for clinical uses.


    Shake and bake. Gaussian accelerated molecular dynamics simulations and state-of-the-art supercomputing resources reveal the conformational change of the HNH domain (green) from its inactive to active state. Courtesy Giulia Palermo, McCammon Lab, UC San Diego.

    “Although the CRISPR-Cas9 system is rapidly revolutionizing life sciences toward a facile genome editing technology, structural and mechanistic details underlying its function have remained unknown,” says Giulia Palermo, a postdoctoral scholar with the UC San Diego Department of Pharmacology and lead author of the study [PNAS].

    See the full article here
    .

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    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
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