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  • richardmitnick 2:47 pm on December 18, 2017 Permalink | Reply
    Tags: "We noticed that after the initial transfer the nanomaterial would still luminesce in a delayed fashion", , , NC State University, Optoelectronics,   

    From NC State: “Researchers show thermally activated delayed photoluminescence from semiconductor nanocrystals” 

    NC State bloc

    North Carolina State University

    This post is dedicated to J.M. in Maryland, because she loves pretty pictures.

    1
    Pyrenecarboxylic acid-functionalized CdSe quantum dots undergo thermally activated delayed photoluminescence. Image: Cedric Mongin

    December 18, 2017
    Tracey Peake
    tracey_peake@ncsu.edu
    919.515.6142

    Researchers from North Carolina State University have found that the transfer of triplet excitons from nanomaterials to molecules also creates a feedback mechanism that returns some energy to the nanocrystal, causing it to photoluminesce on long time scales. The mechanism can be adjusted to control the amount of energy transfer, which could be useful in optoelectronic applications.

    Felix N. Castellano, Goodnight Innovation Distinguished Chair of Chemistry at NC State, had previously shown that semiconductor nanocrystals could transfer energy to molecules, thereby extending their excited state lifetimes long enough for them to be useful in photochemical reactions.

    In a new contribution, Castellano and Cédric Mongin, a former postdoctoral researcher currently an assistant professor at École normale supérieure Paris-Saclay in France, have shown that not only does the transfer of triplet excitons extend excited state lifetimes, but also that some of the energy gets returned to the original nanomaterial in the process.

    “When we looked at triplet exciton transfers from nanomaterials to molecules, we noticed that after the initial transfer the nanomaterial would still luminesce in a delayed fashion, which was unexpected,” says Castellano. “So we decided to find out what exactly was happening at the molecular level.”

    Castellano and Mongin utilized cadmium selenide (CdSe) quantum dots as the nanomaterial and pyrenecarboxylic acid (PCA) as the acceptor molecule. At room temperature, they found that the close proximity of the relevant energy levels created a feedback mechanism that thermally repopulated the CdSe excited state, causing it to photoluminesce.

    Taking the experiment one step further, the researchers then systematically varied the CdSe-PCA energy gap by changing the size of the nanocrystals. This resulted in predictable changes to the resultant excited state lifetimes. They also examined this process at different temperatures, yielding results consistent with a thermally activated energy transfer mechanism.

    “Depending on relative energy separation, the system can be tuned to behave more like PCA or more like the CdSe nanoparticle,” says Castellano. “It’s a control dial for the system. We can make materials with unique photoluminescent properties simply by controlling the size of the nanoparticle and the temperature of the system.”

    The work appears in Nature Chemistry, and was supported by the Air Force Office of Scientific Research (FA9550-13-1-0106) and the U.S. Department of Energy (DE-SC0011979). Mongin is first author and Castellano is corresponding author. Pavel Moroz and Mikhail Zamkov of Bowling Green State University also contributed to the work.

    See the full article here .

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    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 4:36 pm on December 11, 2017 Permalink | Reply
    Tags: , , , NC State University, Researchers Find Simpler Way to Deposit Magnetic Iron Oxide onto Gold Nanorods   

    From NC State and MIT: “Researchers Find Simpler Way to Deposit Magnetic Iron Oxide onto Gold Nanorods” 

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    North Carolina State University

    MIT News
    MIT Widget

    MIT News

    December 11, 2017
    Joe Tracy, NC State
    919.513.2623

    Matt Shipman, NC State
    919.515.6386

    1
    Mixing silica-overcoated gold nanorods (left) and iron oxide nanoparticles (center) yields iron oxide-overcoated gold nanorods (right). Credit: Brian Chapman.

    Researchers from North Carolina State University and MIT have found a simpler way to deposit magnetic iron oxide (magnetite) nanoparticles onto silica-coated gold nanorods, creating multifunctional nanoparticles with useful magnetic and optical properties.

    Gold nanorods have widespread potential applications because they have a surface plasmon resonance – meaning they can absorb and scatter light. And by controlling the dimensions of the nanorods, specifically their aspect ratio (or length divided by diameter), the wavelength of the absorbed light can be controlled. This characteristic makes gold nanorods attractive for use in catalysis, security materials and a host of biomedical applications, such as diagnostics, imaging, and cancer therapy. The fact that the magnetite-gold nanoparticles can also be manipulated using a magnetic field enhances their potential usefulness for biomedical applications, such as diagnostic tools or photothermal therapeutics.

    “The approach we outline in our new paper is simple, likely making it faster and less expensive than current techniques for creating these nanoparticles – on a small scale or a large one,” says Joe Tracy, an associate professor of materials science and engineering at NC State and corresponding author of a paper on the work.

    The new technique uses an approach called heteroaggregation. Silica-coated gold nanorods are dispersed in ethanol, a polar solvent. In ethanol, the hydrogen atoms are partially positively charged, and the oxygen atoms are partially negatively charged. The magnetite nanoparticles are dispersed in hexanes, a non-polar solvent, where the charges are not separated. When the two solutions are mixed, the magnetite nanoparticles bind to the gold nanorods – and the resulting magnetite-gold nanoparticles are removed from the solvent using a simple centrifugation process.

    “We are able to take pre-synthesized, silica-coated gold nanorods and iron oxide nanoparticles and then combine them,” says Brian Chapman, a Ph.D. student at NC State and lead author of the paper. “This is simpler than other techniques, which rely on either growing iron oxide nanoparticles on gold nanorods or using molecular cross-linkers to bind the iron to the silica coating of the nanorods.”

    “Our approach also results in highly uniform nanoparticles,” Tracy says. “And by incorporating ligands called PEG-catechols, the resulting nanoparticles can be dispersed in water. This makes them more useful for biomedical applications.

    “These are interesting, and potentially very useful, multifunctional nanoparticles,” Tracy adds. “And hopefully this work will facilitate the development of applications that capitalize on them.”

    The paper, Heteroaggregation Approach for Depositing Magnetite Nanoparticles onto Silica-Overcoated Gold Nanorods, is published in the journal Chemistry of Materials. The paper was co-authored by Wei-Chen Wu, a former Ph.D. student at NC State; and Qiaochu Li and Niels Holten-Andersen of MIT. The work was done with support from the National Science Foundation under grants DMR-1121107, DMR-1056653, and CBET-1605699.

    See the full article here .

    Please help promote STEM in your local schools.

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    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 1:43 pm on June 8, 2017 Permalink | Reply
    Tags: , , Caren Cooper, NC State University, ,   

    From NC State via WCG: Women in STEM: “Leadership in Public Science: Meet Caren Cooper” Revised and Improved 

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    North Carolina State University


    Presented by World Community Grid

    June 7, 2017
    Matt Shipman

    This is one in a series of five Q&As with the members of NC State’s Leadership in Public Science faculty cluster. Read more about the cluster.

    Caren Cooper wrote the book on citizen science. Literally. That made her a natural fit for NC State’s Leadership in Public Science effort.

    Cooper is an ecologist whose work involves collaborating with bird lovers to learn more about wildlife and ecosystems in urban, suburban and rural environments. She is assistant head of the biodiversity research lab at the North Carolina Museum of Natural Sciences and a research associate professor in NC State’s Department of Forestry and Environmental Resources. She came to Raleigh from the Cornell Lab of Ornithology, but it was a bit of a homecoming; Cooper got her undergrad degree at NC State.

    As for her book, citizen science is right there in the title: Citizen Science: How Ordinary People Are Changing the Face of Discovery. You can also see Cooper talk about citizen science and its relationship to public science by checking out her TEDx talk online.

    1
    Caren Cooper

    Learn about what Cooper is working on.

    What does your research focus on?

    I’m interested in a variety of natural processes and human behaviors related to environmental change. I value and use citizen science approaches to investigate natural-human systems and map environmental changes and disparities. I enjoy exploring the potential of citizen science to manage natural resources and to bring varied hobby groups into citizen science, like birders, nest box monitors, duck hunters, pigeon fanciers, etc.

    What does “public science” mean to you, and how does it factor into your work?

    To me, public science refers to science that is transparent, out in the open and accessible to all. I think of citizen science as networks of volunteers helping to advance knowledge and public scientists as professionals building and tending those networks and helping people make meaning of the collective information.

    I think successful public scientists must be familiar with the teamwork of designing and implementing citizen science, public communication of science in many forms and open science practices from the start of a research project to its completion and again with the next iteration. Citizen science often looks like it is simply people volunteering in service to science, but in a public science context, it is really about bridging the gap between science and society to make sure that science is in service to humanity.

    What drew you to public science in the first place?

    When I became a scientist, I liked to do all parts of scientific research myself. That’s how I defined being a scientist: someone who can carry out research independently. My husband and I started a family while I was pursing my Ph.D. Field work became difficult, and my priorities shifted.

    I was drawn to citizen science at first because it was a way for birdwatchers to collect all the data that I would ever need. Unexpectedly, it also sparked my interest in the social sciences, science communication and open science. I found it puzzling as to why scientists regarded citizen science poorly and typically failed to recognize its many contributions.

    At first I was bothered by the lack of acknowledging lay expertise and the efforts and abilities of volunteers. Then I became bothered by the lack of acknowledging the limits of scientific inquiry — there are some big questions that scientists can’t answer by working alone. Citizen science is a social movement among volunteers within science, which I find fascinating and exciting. Public science is a movement among professionals to support citizen science and other forms of public engagement in science, while also supporting the engagement of scientists with the public and in the public sphere.

    What sort of public science projects are you working on at NC State?

    I’m helping develop SciStarter.com as a central hub for people to find and participate in citizen science projects around the world. We are also designing SciStarter with tools to help projects become more sustainable by sharing resources related to recruitment, retention and communication with volunteer communities. With SciStarter, we will also help advance understanding of the design and outcomes of citizen science.

    I run a citizen science project called Sparrow Swap, which partners with volunteers who monitor nest boxes and view house sparrows as a pest species. They collect house sparrow eggs according to one of four protocol options and donate those eggs to the collections at the NC Museum of Natural Sciences, where my lab is based. We use the eggs to study geographic variation in eggshell patterns and color, and to determine whether eggshells can be used as a biological tool for identifying and mapping environmental contaminants. Volunteers also collect data on the effectiveness of different management options, including swapping in egg replicas (which we paint at the museum) for real eggs and hopefully reducing house sparrow reproduction and their disturbance of native nesting birds. We are developing an online interactive guide to the basics of wildlife management principles.

    We are soon launching Sound Around Town in partnership with other universities to support soundscape studies led by the National Park Service (NPS). In Sound Around Town, volunteers will be able to borrow sound recording equipment from their local library and deploy the equipment in their backyards to provide soundscape data to the NPS. They will also use our listening app to ground-truth the recordings and provide information on their feelings and perceptions of each type of sound they identify. Though the equipment loans through libraries will be available only in select cities, we hope volunteers across the country will use the listening app in many urban and residential soundscapes. I’m interested in disparities among communities in noise pollution, which is a combination of actual soundscapes and perceptions of sounds.

    We are also starting to explore the potential of a citizen science project related to finding feather-degrading bacteria.

    As a public science cluster, in collaboration with the libraries, we want to make NC State a citizen science campus in which students campuswide have abundant opportunities to do citizen science as part of their campus life.

    See the full article here .

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    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
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    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

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  • richardmitnick 9:35 pm on March 3, 2017 Permalink | Reply
    Tags: NC State University, , ,   

    From NC State via phys.org: “Calculations show close Ia supernova should be neutrino detectable offering possibility of identifying explosion type” 

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    North Carolina State University

    phys.org

    phys.org

    1
    Density contour plots including deflagration (white) and detonation (green) surfaces. Credit: arXiv:1609.07403 [astro-ph.HE]

    A team of researchers at North Carolina State University has found that current and future neutrino detectors placed around the world should be capable of detecting neutrinos emitted from a relatively close supernova. They also suggest that measuring such neutrinos would allow them to explain what goes on inside of a star during such an explosion—if the measurements match one of two models that the team has built to describe the inner workings of a supernova.

    Supernovae have been classified into different types depending on what causes them to occur—one type, called a la supernova, occurs when a white dwarf pulls in enough material from a companion, eventually triggering carbon fusion, which leads to a massive explosion. Researchers here on Earth can see evidence of a supernova by the light that is emitted. But astrophysicists would really like to know more about the companion and the actual process that occurs inside the white dwarf leading up to the explosion—and they believe that might be possible by studying the neutrinos that are emitted.

    In this new effort, a team led by Warren Wright calculated that neutrinos from a relatively nearby supernova should be detectable by current sensors already installed and working around the planet and by those that are in the works. Wright also headed two teams that have each written a paper describing one of two types of models that the team has built to describe the process that occurs in the white dwarf leading up to the explosion—both teams have published their work in the journal Physical Review Letters.

    The first model is called the deflagration-to-detonation transition; the second, the gravitationally confined detonation. Both are based on theory regarding interactions inside of the star and differ mostly in how spherically symmetric they are. The two types would also emit different kinds and amounts of neutrinos, which is why the team is hoping that the detectors capable of measuring them will begin to do so. That would allow the teams to compare their models against real measurable data, and in so doing, perhaps finally offer some real evidence of what occurs when stars explode.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 5:31 pm on December 1, 2016 Permalink | Reply
    Tags: , , MoS2, NC State University   

    From NC State: “New Findings Boost Promise of Molybdenum Sulfide for Hydrogen Catalysis” 

    NC State bloc

    North Carolina State University

    December 1, 2016
    Linyou Cao
    919.515.5407
    linyou_cao@ncsu.edu

    Matt Shipman
    919.515.6386
    matt_shipman@ncsu.edu

    1

    Researchers from North Carolina State University, Duke University and Brookhaven National Laboratory have found that molybdenum sulfide (MoS2) holds more promise than previously thought as a catalyst for producing hydrogen to use as a clean energy source. Specifically, the researchers found that the entire surface of MoS2 can be used as a catalyst, not just the edges of the material.

    “The key finding here is that the intrinsic catalytic performance of MoS2 is much better than the research community thought,” says Linyou Cao, an associate professor of materials science and engineering at NC State and senior author of a paper describing the work. “We’re optimistic that this can be a step toward making hydrogen a larger part of our energy portfolio.”

    Hydrogen promises clean energy, producing only water as a byproduct. But to create hydrogen for use as a clean energy source, ideally you’d be able to isolate the hydrogen gas from water – with the only byproduct being oxygen.

    However, the key to creating hydrogen from water – a process called hydrogen evolution – is an efficient catalyst. Currently, the best catalyst is platinum, which is too expensive for widespread use.

    Another candidate for a hydrogen evolution catalyst is MoS2, which is both inexpensive and abundant. But it has long been thought that MoS2 is of limited utility, based on the conventional wisdom that only the edges of MoS2 act as catalysts – leaving the bulk of the material inactive.

    But the new findings from NC State, Duke and Brookhaven show that the surface of MoS2 can be engineered to maximize the catalytic efficiency of the material. And the key to this efficiency is the number of sulfur vacancies in the MoS2.

    If you think of the crystalline structure of MoS2 as a grid of regularly spaced molybdenum and sulfur atoms, a sulfur vacancy is what happens when one of those sulfur atoms is missing.

    “We found that these sulfur vacancies attract the hydrogen atoms in water at just the right strength: the attraction is strong enough pull the hydrogen out of the water molecule, but is then weak enough to let the hydrogen go,” says Cao.

    The researchers also found that the grain boundaries of MoS2 , which have been speculated by the research community to be catalytically active for hydrogen evolution, may only provide trivial activity. Grain boundaries are the boundaries between crystalline domains.

    The findings point to a new direction for improving the catalytic performance of MoS2 . Currently, the most common way is to increase the number of edge sites, because of the conventional wisdom that only the edge sites are catalytically active.

    “Our result indicates that grain boundaries should not be the factor to consider when thinking about improving catalytic activity,” Cao says. “The best way to improve the catalytic activities is to engineer sulfur vacancies. The edges of MoS2 are still twice as efficient at removing hydrogen atoms compared to the sulfur vacancies. But it’s difficult to create a high density of edges in MoS2 – a lot of the material’s area is wasted – whereas a large number of sulfur vacancies can be engineered uniformly across the material.”

    The researchers have also found that there is a “sweet spot” for maximizing the catalytic efficiency of MoS2 .

    “We get the best results when between 7 and 10 percent of the sulfur sites in MoS2 are vacant,” Cao says. “If you go higher or lower than that range, catalytic efficiency drops off significantly.”

    Additionally, the researchers found that the crystalline quality of MoS2 is important to optimize the catalytic activity of the sulfur vacancies. The sulfur vacancies in high crystalline quality MoS2 showed better efficiency than those in low crystalline quality MoS2 , even when the densities of the vacancies are the same.

    “In order to get the best output from sulfur vacancies, the crystalline quality of MoS2 needs to be very high,” says Guoqing Li, a Ph.D. student at NC State and lead author of the paper. “The ideal scenario would be 7 to 10 percent sulfur vacancies uniformly distributed in a single crystalline MoS2 film.”

    The work was done using MoS2 thin films that are only three atoms thick. Using these engineered thin films, the researchers were able to achieve catalytic efficiency comparable to previous MoS2 technologies that relied on having two or three orders of magnitude more surface area.

    “We now know that MoS2 is a more promising catalyst than we anticipated, and are fine-tuning additional techniques to further improve its efficiency,” Cao says. “Hopefully, this moves us closer to making a low-cost catalyst that is at least as good as platinum.”

    The paper, All the Catalytic Active Sites of MoS2 for Hydrogen Evolution,” is published in the Journal of the American Chemical Society. The paper was co-authored by Yifei Yu, David Peterson, Abdullah Zafar, Raj Kumar, Frank Hunte and Steve Shannon of NC State; Du Zhang, Stefano Curtarolo and Weitao Yang of Duke; and Qiao Qiao and Yimei Zhu of Brookhaven National Lab.

    The work was done with support from the Department of Energy’s Office of Science, under grants DE-SC0012575 and DE-SC0012704, as well as by the National Science Foundation under grant PHY1338917.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

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    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 8:09 am on June 14, 2016 Permalink | Reply
    Tags: , , , , NC State University   

    From NC State: “What Is CRISPR? And How Can it Be Used to Turn Genes ‘Off’?” 

    NC State bloc

    North Carolina State University

    1

    June 13, 2016
    Matt Shipman

    CRISPR systems have been a hot research topic since they were shown to have utility as genetic engineering tools in 2012. And they’re often explained in a way that most folks can understand. But those explanations often overlook key details – like the fact that scientists are still in the process of discovering the fundamental rules of how these systems work.

    For example, here’s a simplified explanation: CRISPR-Cas systems protect bacteria from invaders such as viruses. They do this by creating small strands of RNA that match DNA sequences specific to a given invader. When those CRISPR RNAs find a match, they unleash Cas proteins that chop up the invader’s DNA, preventing it from replicating.

    But of course it’s more complex than that. For example, there are six different types of CRISPR systems (that we know of). One of the most widely-studied CRISPR systems is CRISPR-Cas9, which is a Type II CRISPR system.

    But the most common CRISPR systems in nature are Type I. And new research from NC State is shedding light on some of the fundamental rules that govern Type I CRISPR systems – such as how long that CRISPR RNA can be, and how changing the length of the CRISPR RNA affects the behavior of the system.

    To learn more, we talked to Chase Beisel and Michelle Luo, who recently published a paper on the work in Nucleic Acids Research, in collaboration with two groups at Montana State University. Beisel is an assistant professor of chemical and biomolecular engineering at NC State; Luo is a Ph.D. student in Beisel’s lab.

    The Abstract: Why are Type I CRISPR systems of particular interest?
    Michelle Luo1
    Michelle Luo

    Michelle Luo: As you mentioned, Type I systems are the most common type of CRISPR-Cas systems. They account for over half of known systems. This is of particular interest as we look into co-opting an organism’s own system for other purposes. While CRISPR-Cas9 is undeniably a revolutionary genetic tool, it relies on importing this foreign Cas9 protein into an organism. This is a non-trivial task. However, if you use an organism’s own CRISPR-Cas proteins, as shown in our earlier work, you can avoid the challenges of expressing a non-natural protein. Because Type I systems are so prevalent, they offer a promising route to explore how a natural CRISPR-Cas system can be exploited for other means.

    The Abstract: In your recent work, you were evaluating how and whether you could modify the RNA in Type I CRISPR systems. Specifically, you were looking at whether you could modify the length of RNA in Type I CRISPR systems. Why would you want to change the length of the RNA?

    Luo: Two years ago, a number of papers were published detailing the crystal structures of Type I protein complexes that bind and help degrade target DNA. These publications hinted at the CRISPR RNA serving as a scaffold to assemble the different proteins in the complex. In other words, the RNA serves as a framework for these proteins to grab onto. Thus, we hypothesized that if we changed the length of the CRISPR RNA, we could change the size and composition of the Type I protein complex, and possibly the complex’s behavior.

    The Abstract: How, or why, might expanding the protein complexes used in DNA recognition be useful?
    Chase Beisel2
    Chase Beisel

    Chase Beisel: Going into the project, we didn’t know if the longer RNAs would allow the complex to even assemble, let alone function properly. We were surprised to find that the longer RNAs still formed a stable complex that could bind and direct the cutting of DNA. Because this complex is larger and recognizes a longer target sequence, we originally envisioned that the complex could be used for more specific DNA editing or for controlling gene expression.

    The Abstract: When I think of CRISPR, I think of a system that either leaves DNA alone or cuts it up. What do you mean when you say that changing the length of the RNA is more effective at gene repression?

    Luo: Your summary is on point. Normally, CRISPR-Cas systems survey the DNA landscape, and if they detects a target, they will cut up the DNA with tiny molecular scissors. If the target is not identified, the DNA will be left alone. Our earlier work demonstrated that we can prevent the cutting of the DNA by removing the scissors from the equation. We do this by deleting the cas3 gene from the genomic Type I locus. Now, instead of cutting the DNA, the CRISPR-Cas system simply binds the DNA. If we direct these modified systems to a gene, it will block the expression of that gene. Our most recent work shows that changing the length of the RNA can affect how strongly that silencing occurs. For certain regions, the longer the CRISPR RNA, the stronger the repression.

    The Abstract: Does that make the CRISPR system more specific? I.e., does it allow the system to be more targeted in terms of the DNA it “attacks”?

    Beisel: We wondered the same thing. We did in fact explore how longer RNAs impact specificity as part of the publication, although the results were mixed. On one hand, more of the RNA was involved in base pairing, where more base pairing would necessarily mean greater specificity. On the other hand, we found the longer RNAs were accommodating to mismatches with the target sequence, suggesting weaker specificity. In the end, more experiments will be needed to explore the question of specificity and how it impacts any downstream uses of Type I systems.

    The Abstract: How might that gene repression function be used? Are there any potential applications?

    Luo: Absolutely! This is particularly promising for metabolic engineering. If you want to make a microbial factory to produce a valuable product of interest, such as a biofuel, you have to alter the metabolism of an organism. This requires overexpressing genes that lead to production and turning off genes that compete with production. Our system allows researchers to turn off genes in a way that is potent, site-specific, reversible, and multiplexed. Our latest discovery suggests that you can fine-tune the extent of CRISPR-based gene repression simply by altering the length of the CRISPR RNA. That’s what our recent paper in Nucleic Acids Research is about.

    The Abstract: What are the future directions for this research?

    Beisel: Aside from the applications Michelle mentioned, we’re interested in why nature only uses RNA of a fixed length, given that longer RNAs make perfectly functional complexes. We’re also interested in whether this phenomenon applies across the many different flavors of Type I systems, from those that use far fewer proteins in the complex to those found in organisms living at extreme temperatures.

    See the full article here .

    Please help promote STEM in your local schools.

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    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 11:08 am on December 15, 2015 Permalink | Reply
    Tags: , , NC State University, RiboScan   

    From NC State: “Student Project Evolves Into New Tool for the Biotech Industry” 

    NC State bloc

    North Carolina State University

    December 11, 2015
    Matt Shipman

    1
    Scott Vu

    When Scott Vu started working on a computer science research project as a teenager, he didn’t realize it would lead him down a path to earning a Ph.D. in biomedical engineering and launching a company designed to help the biotechnology industry operate more efficiently.

    But Vu’s story has been anything but typical.

    At the age of 4, he and his family were smuggled out of Vietnam on a boat. “Escaping,” Vu says. At the age of 15, he enrolled at NC State University as a full-time student, working toward a triple major in computer science, computer engineering and electrical engineering.

    2
    Joseph Thomas, Scott Vu and William Glauser (from left to right).

    As an undergraduate, Vu began working with his mentor, Donald Bitzer, on a project aimed at creating a computer-based biophysical model to understand how to manipulate genes in bacteria to get those bacteria to produce specific proteins that they would not normally produce. The idea was that these bacteria would offer an easier, less expensive way to create proteins for use in manufacturing everything from biofuels to antibiotics.

    Vu’s undergraduate project grew into a Ph.D. dissertation as Vu pursued a doctorate in the joint biomedical engineering program at NC State and UNC-Chapel Hill. In graduate school, Vu learned myriad life science techniques he needed to test the model in vivo, conducting the necessary experiments in the lab of NC State microbiologist Eric Miller with the help of undergraduate research assistants Adriano Bellotti, Chris Gabriel and Hayden Brochu.

    Incorporating techniques from computer science, biophysics, molecular biology and microbiology, Vu was ultimately able to not only fine-tune his model, but to use the model to “optimize” genes in bacteria so that they would produce many desired proteins quickly and accurately.

    Creating individual proteins is important to biotech companies because proteins are used across a broad range of industrial applications. For example, proteins can be used in wastewater treatment, laundry detergent, winemaking, and to develop drugs for treating diseases like diabetes and cancer.

    In late 2012, in the midst of his research on protein synthesis, Vu was inspired by a talk with Mladen Vouk, one of his Ph.D. committee advisers, to launch a venture and pursue a patent for the biophysical model he had developed. Thus began the lengthy process of learning what he needed to know about the business world.

    Vu began working with NC State’s Office of Technology Transfer and took two courses that he credits with setting him on the right track. One was a class with Steve Markham in NC State’s Poole College of Management, where he met fellow students William Glauser and Joseph Thomas, who would become co-founders of his company, RiboWiz Scientific. The other course was the “FastTrac” entrepreneurial training program with the Council for Entrepreneurial Development.

    “These courses taught me what I needed to know about bringing an idea to the market – doing market research, estimating costs and profits, developing a business plan, pitching ideas to investors,” Vu says. “It was eye-opening.”

    Ultimately, Vu created RiboScan™, a web-based tool based on the model he started developing as an undergraduate. A patent was submitted on Vu’s technology before he completed his Ph.D., and he has already incorporated his company. The company, RiboWiz, is now seeking industry partners to commercialize the technology.

    “We only incorporated RiboWiz in October, but we are already able to work with customers,” Vu says. “We are looking forward to using our technology to help industry partners produce proteins they’ve been unable to make in the past. And we’re also planning to file Small Business Innovation Research grant proposals, which would support future research to improve our model. We plan on expanding the model to predict and maximize protein production in eukaryotes and addressing issues related to protein aggregation caused by the misfolding of proteins during synthesis.

    “I’m ready to go to work.”

    A paper on the biophysical model, Modeling ribosome dynamics to optimize heterologous protein production in Escherichia coli,” was published in the Proceedings of the 2014 IEEE Global Conference on Signal and Information Processing. The paper was co-authored by A.A. Bellotti, C.J. Gabriel, H.N. Brochu, E.S. Miller, D.L. Bitzer, and M.A. Vouk.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 9:12 pm on December 3, 2015 Permalink | Reply
    Tags: , NC State University, Q Carbon   

    From NC State: “Researchers Find New Phase of Carbon, Make Diamond at Room Temperature” 

    NC State bloc

    North Carolina State University

    November 30, 2015
    Jay Narayan | 919.515.7874
    Matt Shipman | 919.515.6386

    1
    This is a scanning electron microscopy image of microdiamonds made using the new technique.

    Researchers from North Carolina State University have discovered a new phase of solid carbon, called Q-carbon, which is distinct from the known phases of graphite and diamond. They have also developed a technique for using Q-carbon to make diamond-related structures at room temperature and at ambient atmospheric pressure in air.

    Phases are distinct forms of the same material. Graphite is one of the solid phases of carbon; diamond is another.

    “We’ve now created a third solid phase of carbon,” says Jay Narayan, the John C. Fan Distinguished Chair Professor of Materials Science and Engineering at NC State and lead author of three papers describing the work. “The only place it may be found in the natural world would be possibly in the core of some planets.”

    Q-carbon has some unusual characteristics. For one thing, it is ferromagnetic – which other solid forms of carbon are not.

    “We didn’t even think that was possible,” Narayan says.

    In addition, Q-carbon is harder than diamond, and glows when exposed to even low levels of energy.

    “Q-carbon’s strength and low work-function – its willingness to release electrons – make it very promising for developing new electronic display technologies,” Narayan says.

    But Q-carbon can also be used to create a variety of single-crystal diamond objects. To understand that, you have to understand the process for creating Q-carbon.

    Researchers start with a substrate, such as such as sapphire, glass or a plastic polymer. The substrate is then coated with amorphous carbon – elemental carbon that, unlike graphite or diamond, does not have a regular, well-defined crystalline structure. The carbon is then hit with a single laser pulse lasting approximately 200 nanoseconds. During this pulse, the temperature of the carbon is raised to 4,000 Kelvin (or around 3,727 degrees Celsius) and then rapidly cooled. This operation takes place at one atmosphere – the same pressure as the surrounding air.

    The end result is a film of Q-carbon, and researchers can control the process to make films between 20 nanometers and 500 nanometers thick.

    By using different substrates and changing the duration of the laser pulse, the researchers can also control how quickly the carbon cools. By changing the rate of cooling, they are able to create diamond structures within the Q-carbon.

    “We can create diamond nanoneedles or microneedles, nanodots, or large-area diamond films, with applications for drug delivery, industrial processes and for creating high-temperature switches and power electronics,” Narayan says. “These diamond objects have a single-crystalline structure, making them stronger than polycrystalline materials. And it is all done at room temperature and at ambient atmosphere – we’re basically using a laser like the ones used for laser eye surgery. So, not only does this allow us to develop new applications, but the process itself is relatively inexpensive.”

    And, if researchers want to convert more of the Q-carbon to diamond, they can simply repeat the laser-pulse/cooling process.

    If Q-carbon is harder than diamond, why would someone want to make diamond nanodots instead of Q-carbon ones? Because we still have a lot to learn about this new material.

    “We can make Q-carbon films, and we’re learning its properties, but we are still in the early stages of understanding how to manipulate it,” Narayan says. “We know a lot about diamond, so we can make diamond nanodots. We don’t yet know how to make Q-carbon nanodots or microneedles. That’s something we’re working on.”

    NC State has filed two provisional patents on the Q-carbon and diamond creation techniques.

    The work is described in two papers, both of which were co-authored by NC State Ph.D. student Anagh Bhaumik. Novel Phase of Carbon, Ferromagnetism and Conversion into Diamond was published online Dec. 2 in the Journal of Applied Physics. Direct conversion of amorphous carbon into diamond at ambient pressures and temperatures in air was published Oct. 7 in the journal APL Materials. The work was supported in part by the National Science Foundation, under grant number DMR-1304607.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    NC State campus

    NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 10:42 am on March 24, 2015 Permalink | Reply
    Tags: , , NC State University   

    From NC State: “Shrinking Habitats Have Adverse Effects on World Ecosystems” 

    NC State bloc

    North Carolina State University

    1
    A new study shows habitat fragmentation has harmful effects to world ecosystems. Researchers studied fragmentation at seven sites across five continents. Photo courtesy of Nick Haddad, NC State University

    An extensive study of global habitat fragmentation – the division of habitats into smaller and more isolated patches – points to major trouble for a number of the world’s ecosystems and the plants and animals living in them.

    The study shows that 70 percent of existing forest lands are within a half-mile of the forest edge, where encroaching urban, suburban or agricultural influences can cause any number of harmful effects – like the losses of plants and animals.

    The study also tracks seven major experiments on five continents that examine habitat fragmentation and finds that fragmented habitats reduce the diversity of plants and animals by 13 to 75 percent, with the largest negative effects found in the smallest and most isolated fragments of habitat.

    The study, led by a researcher from North Carolina State University and involving about two dozen researchers across the globe, is reported today in a paper published in Science Advances.

    The researchers assembled a map of global forest cover and found very few forest lands unencumbered by some type of human development.

    “It’s no secret that the world’s forests are shrinking, so this study asked about the effects of this habitat loss and fragmentation on the remaining forests,” said Dr. Nick Haddad, William Neal Reynolds Distinguished Professor of Biological Sciences at NC State and the corresponding author of the paper.

    “The results were astounding. Nearly 20 percent of the world’s remaining forest is the distance of a football field – or about 100 meters – away from a forest edge. Seventy percent of forest lands are within a half-mile of a forest edge. That means almost no forest can really be considered wilderness.”

    The study also examined seven existing major experiments on fragmented habitats currently being conducted across the globe; some of these experiments are more than 30 years old.

    Covering many different types of ecosystems, from forests to savannas to grasslands, the experiments combined to show a disheartening trend: Fragmentation causes losses of plants and animals, changes how ecosystems function, reduces the amounts of nutrients retained and the amount of carbon sequestered, and has other deleterious effects.

    “The initial negative effects were unsurprising,” Haddad said. “But I was blown away by the fact that these negative effects became even more negative with time. Some results showed a 50 percent or higher decline in plant and animals species over an average of just 20 years, for example. And the trajectory is still spiraling downward.”

    Haddad points to some possible ways of mitigating the negative effects of fragmentation: conserving and maintaining larger areas of habitat; utilizing landscape corridors, or connected fragments that have shown to be effective in achieving higher biodiversity and better ecosystem function; increasing agricultural efficiency; and focusing on urban design efficiencies.

    “The key results are shocking and sad,” Haddad said. “Ultimately, habitat fragmentation has harmful effects that will also hurt people. This study is a wake-up call to how much we’re affecting ecosystems – including areas we think we’re conserving.”

    The study was supported by the National Science Foundation.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    NC State Campus

    As a land-grant institution, NC State itself was born as an idea: that higher education should bring economic, societal and intellectual prosperity to the masses. From our origins teaching the agricultural and mechanical arts, we’ve grown to become a pre-eminent research enterprise that advances knowledge in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

     
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