Advanced Science Research Center

New York City, NY, United States

Advanced Science Research Center

New York City, NY, United States
SEARCH FILTERS
Time filter
Source Type

Ocasio V.J.,Southwestern Medical Center | Correa F.,Southwestern Medical Center | Correa F.,Advanced Science Research Center | Gardner K.H.,Southwestern Medical Center | And 2 more authors.
Biochemistry | Year: 2015

To survive and adapt to environmental changes, bacteria commonly use two-component signaling systems. Minimally, these pathways use histidine kinases (HKs) to detect environmental signals, harnessing these to control phosphorylation levels of receiver (REC) domains of downstream response regulators that convert this signal into physiological responses. Studies of several prototypical REC domains suggest that phosphorylation shifts these proteins between inactive and active structures that are globally similar and well-folded. However, it is unclear how globally these findings hold within REC domains in general, particularly when they are considered within full-length proteins. Here, we present EL-LovR, a full-length REC-only protein that is phosphorylated in response to blue light in the marine α-proteobacterium, Erythrobacter litoralis HTCC2594. Notably, EL-LovR is similar to comparable REC-only proteins used in bacterial general stress responses, where genetic evidence suggests that their potent phosphatase activity is important to shut off such systems. Size exclusion chromatography, light scattering, and solution NMR experiments show that EL-LovR is monomeric and unfolded in solution under conditions routinely used for other REC structure determinations. Addition of Mg2+ and phosphorylation induce progressively greater degrees of tertiary structure stabilization, with the solution structure of the fully activated EL-LovR adopting the canonical receiver domain fold. Parallel functional assays show that EL-LovR has a fast dephosphorylation rate, consistent with its proposed function as a phosphate sink that depletes the HK phosphoryl group, promoting the phosphatase activity of this enzyme. Our findings demonstrate that EL-LovR undergoes substantial ligand-dependent conformational changes that have not been reported for other RRs, expanding the scope of conformational changes and regulation used by REC domains, critical components of bacterial signaling systems. © 2015 American Chemical Society.


Deshko Y.,City College of New York | Krusin-Elbaum L.,City College of New York | Menon V.,City College of New York | Khanikaev A.,Queens College, City University of New York | Trevino J.,Advanced Science Research Center
Optics Express | Year: 2016

We investigate the propagation of surface plasmon polaritons (SPPs) in thin films of topological insulators. Cases of single films and multilayered stacks are analyzed. The materials considered are second generation three dimensional topological insulators Bi2Se3, Bi2Te3, and Sb2Te3. Dispersion relations and propagation lengths of SPPs are estimated numerically, taking into account the variation of bulk dielectric functions of topological insulators, as well as substrate, using the Drude-Lorentz model. The key factors affecting propagation length are identified and experimental modifications for tuning the dispersion relations are proposed. The apparent discrepancy between the experimental data and previously considered theory is resolved. © 2016 Optical Society of America.


Correa F.,Advanced Science Research Center | Gardner K.H.,Advanced Science Research Center | Gardner K.H.,City College of New York | Gardner K.H.,City University of New York
Cell Chemical Biology | Year: 2016

Information transmission in biological signaling networks is commonly considered to be a unidirectional flow of information between protein partners. According to this view, many bacterial response regulator proteins utilize input receiver (REC) domains to “switch” functional outputs, using REC phosphorylation to shift pre-existing equilibria between inactive and active conformations. However, recent data indicate that output domains themselves also shift such equilibria, implying a “mutual inhibition” model. Here we use solution nuclear magnetic resonance to provide a mechanistic basis for such control in a PhyR-type response regulator. Our structure of the isolated, non-phosphorylated REC domain surprisingly reveals a fully active conformation, letting us identify structural and dynamic changes imparted by the output domain to inactivate the full-length protein. Additional data reveal transient structural changes within the full-length protein, facilitating activation. Our data provide a basis for understanding the changes that REC and output domains undergo to set a default “inactive” state. © 2016 Elsevier Ltd


Brown J.D.,University of Maryland Baltimore County | Summers M.F.,University of Maryland Baltimore County | Johnson B.A.,University of Maryland Baltimore County | Johnson B.A.,One Moon Scientific Inc. | Johnson B.A.,Advanced Science Research Center
Journal of Biomolecular NMR | Year: 2015

The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the 1H NMR and 13C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and 1H and 13C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA 1H and 13C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides. © 2015 Springer Science+Business Media Dordrecht.


Hong F.,Arizona State University | Jiang S.,Arizona State University | Wang T.,Advanced Science Research Center | Liu Y.,Arizona State University | Yan H.,Arizona State University
Angewandte Chemie - International Edition | Year: 2016

Designer DNA architectures with nanoscale geometric controls provide a programmable molecular toolbox for engineering complex nanodevices. Scaffolded DNA origami has dramatically improved our ability to design and construct DNA nanostructures with finite size and spatial addressability. Here we report a novel design strategy to engineer multilayered wireframe DNA structures by introducing crossover pairs that connect neighboring layers of DNA double helices. These layered crossovers (LX) allow the scaffold or helper strands to travel through different layers and can control the relative orientation of DNA helices in neighboring layers. Using this design strategy, we successfully constructed four versions of two-layer parallelogram structures with well-defined interlayer angles, a three-layer structure with triangular cavities, and a 9- and 15-layer square lattices. This strategy provides a general route to engineer 3D framework DNA nanostructures with controlled cavities and opportunities to design host–guest networks analogs to those produced with metal organic frameworks. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim


News Article | October 4, 2016
Site: www.rdmag.com

Research led by Rein Ulijn, Director of the CUNY Advanced Science Research Center (ASRC)'s Nanoscience Initiative and Professor of Chemistry at Hunter College, has paved the way for the development of dynamically-evolving polymers that form spontaneously by adapting to their environment, which may lead to a number of product possibilities including drug delivery, food science and cosmetics, the results of which were published today in Nature Nanotechnology. By allowing these peptides—strings of polymers composed of amino acids—to continuously reorganize their sequences, they will eventually form those polymers that are most suited to the environment at the expense of less favored structures. This method, which is inspired by the principles of evolution, allowed Ulijn's team to identify a range of heretofore unseen peptide-based materials. While previous research in peptide nanotechnology centered on chance discoveries or painstaking design, the new approach allows for unbiased discovery by self-selection of optimized structures. "In our quest to find materials based on biology's building blocks—but which are much simpler-it is difficult to rationally design these materials because there are very many possible permutations that could be explored," Ulijn said. "Instead of designing rationally to improve materials, we've found a way to autonomously evolve," said Charalampos Pappas, first author, and former CUNY ASRC postdoctoral researcher. "We achieve this by having components dynamically connect, rearrange and disconnect, resulting in the spontaneous selection and formation of the most stable self-assembling nanostructures." The paper, entitled "Dynamic peptide libraries for the discovery of supramolecular nanomaterials," is a continuation of Ulijn's research of tunable peptide structures, which have shown great promise in a variety of commercial applications. These include nanospheres which can be biodegradable and could potentially be used in drug delivery applications, as well as nanofibers which form gel-phase materials, that can be used in a variety of applications, including cosmetics or biodegradable plastics that can withstand harsh conditions. The evolution-based peptide discovery method does not yet cover the full range of chemical functionalities present in natural materials and it is currently a time-consuming process. "These issues can potentially be overcome by automation and miniaturization of the process, which is the focus of current research," Ulijn said.


News Article | March 11, 2016
Site: www.nanotech-now.com

Abstract: A team of international scientists led by researchers of the CUNY Advanced Science Research Center (ASRC) and the Politecnico of Milan in Italy has demonstrated a novel approach for designing fully reconfigurable magnetic nanopatterns whose properties and functionality can be programmed and reprogrammed on-demand. The method -- published in Nature Nanotechnology and led by Elisa Riedo, Professor of Physics with the ASRC's Nanoscience Initiative, and Riccardo Bertacco, a professor with the Politenico of Milan--is based on thermal scanning probe lithography and uses a hot nano-tip to perform a highly localized field heating and cooling in antiferromagnetic and ferromagnetic thin films. The hot tip is then used to align the spins in the material in any desired direction with nanoscale resolution. "The proposed technique is straightforward and combines the full reversibility and stability of exchange bias, as the same pattern can be written and reset many times, with the resolution and versatility of scanning probe lithography," said Riedo. "In particular, this work demonstrates how thermal scanning probe lithography is gaining momentum as a key nanofabrication method for the next generation of nanodevices, from biomedical sensing to sprintronics." This approach offers researchers the opportunity to control magnetism at the nanoscale as never before. The authors used this method to fabricate channels where spin waves can propagate. Spin waves are a propagating re-ordering of the magnetization in a material. A new generation of computing and sensing devices can be fabricated based on the propagation of spin waves instead of the more conventional electric current. Bertacco noted these findings will allow for the development of novel metamaterials with finely-tuned magnetic properties, as well as a reconfigurable computing device architectures. "Equally promising is the creation of structures with high response to external magnetic fields, as they can be used as sensors in new architectures of spintronic devices," he said. "The potential target market for these devices is extremely large--especially with the advent of the age of the 'Internet of things'--in which every object has a growing need for integrated sensors and computational capacity." Edoardo Albisetti, postdoctoral research associate at the Politecnico of Milan and the paper's first author, said the new magnetic nanostructure patterning method gives researchers an increased amount of control. "So far, the patterning of magnetic nanostructures has been mainly achieved through irreversible structural or chemical modifications," Albisetti said. "On the contrary, by using this new thermal assisted magnetic scanning probe lithography (tam-SPL) method, the magnetic nanopatterns are fully reconfigurable and obtained without modifying the film chemistry and topography." The ability to draw new meta-magnetic materials opens the way for the development of innovative devices for information processing based on logic cells as well as on the propagation and manipulation of spin waves in magnonic structures. ### The work was supported by the U.S. Department of Energy, the US National Science Foundation, and the Fondazione Cariplo. For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.


News Article | October 4, 2016
Site: phys.org

Research led by Rein Ulijn, Director of the CUNY Advanced Science Research Center (ASRC)'s Nanoscience Initiative and Professor of Chemistry at Hunter College, has paved the way for the development of dynamically-evolving polymers that form spontaneously by adapting to their environment, which may lead to a number of product possibilities including drug delivery, food science and cosmetics, the results of which were published today in Nature Nanotechnology.


News Article | March 10, 2016
Site: www.rdmag.com

A team of international scientists led by researchers of the CUNY Advanced Science Research Center (ASRC) and the Politecnico of Milan in Italy has demonstrated a novel approach for designing fully reconfigurable magnetic nanopatterns whose properties and functionality can be programmed and reprogrammed on-demand. The method—published in Nature Nanotechnology and led by Elisa Riedo, professor of Physics with the ASRC's Nanoscience Initiative, and Riccardo Bertacco, a professor with the Politecnico of Milan—is based on thermal scanning probe lithography and uses a hot nano-tip to perform a highly localized field heating and cooling in antiferromagnetic and ferromagnetic thin films. The hot tip is then used to align the spins in the material in any desired direction with nanoscale resolution. "The proposed technique is straightforward and combines the full reversibility and stability of exchange bias, as the same pattern can be written and reset many times, with the resolution and versatility of scanning probe lithography," said Riedo. "In particular, this work demonstrates how thermal scanning probe lithography is gaining momentum as a key nanofabrication method for the next generation of nanodevices, from biomedical sensing to sprintronics." This approach offers researchers the opportunity to control magnetism at the nanoscale as never before. The authors used this method to fabricate channels where spin waves can propagate. Spin waves are a propagating re-ordering of the magnetization in a material. A new generation of computing and sensing devices can be fabricated based on the propagation of spin waves instead of the more conventional electric current. ​Bertacco noted these findings will allow for the development of novel metamaterials with finely-tuned magnetic properties, as well as a reconfigurable computing device architectures. "Equally promising is the creation of structures with high response to external magnetic fields, as they can be used as sensors in new architectures of spintronic devices," he said. "The potential target market for these devices is extremely large—especially with the advent of the age of the 'Internet of things'—in which every object has a growing need for integrated sensors and computational capacity." Edoardo Albisetti, postdoctoral research associate at the Politecnico of Milan and the paper's first author, said the new magnetic nanostructure patterning method gives researchers an increased amount of control. "So far, the patterning of magnetic nanostructures has been mainly achieved through irreversible structural or chemical modifications," Albisetti said. "On the contrary, by using this new thermal assisted magnetic scanning probe lithography (tam-SPL) method, the magnetic nanopatterns are fully reconfigurable and obtained without modifying the film chemistry and topography." The ability to draw new meta-magnetic materials opens the way for the development of innovative devices for information processing based on logic cells as well as on the propagation and manipulation of spin waves in magnonic structures.


News Article | October 11, 2016
Site: www.materialstoday.com

Research led by Rein Ulijn, director of the CUNY Advanced Science Research Center (ASRC)'s Nanoscience Initiative and professor of chemistry at Hunter College, could pave the way for the development of dynamically-evolving polymers that form spontaneously by adapting to their environment. This research, which is reported in a paper in Nature Nanotechnology, could lead to a number of product possibilities in applications such as drug delivery, food science and cosmetics. Ulijn and his team discovered that if peptides – strings of polymers composed of amino acids – are allowed to continuously reorganize their sequences, they will eventually form polymers that are best suited to their environment, at the expense of less favored structures. Using this method, which is inspired by the principles of evolution, Ulijn's team was able to identify a range of heretofore unseen peptide-based materials. While previous research in peptide nanotechnology has centered on chance discoveries or painstaking design, this new approach allows for the unbiased discovery by self-selection of optimized structures. "In our quest to find materials based on biology's building blocks – but which are much simpler – it is difficult to rationally design these materials because there are very many possible permutations that could be explored," Ulijn said. "Instead of designing rationally to improve materials, we've found a way to autonomously evolve," said Charalampos Pappas, first author and a former CUNY ASRC postdoctoral researcher. "We achieve this by having components dynamically connect, rearrange and disconnect, resulting in the spontaneous selection and formation of the most stable self-assembling nanostructures." This paper is a continuation of Ulijn's research into tunable peptide structures, which have shown great promise in a variety of commercial applications. These include: biodegradable nanospheres for use in drug delivery applications; nanofibers that can form gel-phase materials, which could find use in a variety of applications, including cosmetics; and biodegradable plastics that can withstand harsh conditions. This evolution-based peptide discovery method does not yet cover the full range of chemical functionalities present in natural materials and is currently a time-consuming process. "These issues can potentially be overcome by automation and miniaturization of the process, which is the focus of current research," Ulijn said. This story is adapted from material from CUNY Advanced Science Research Center, with editorial changes made by Materials Today. The views expressed in this article do not necessarily represent those of Elsevier. Link to original source.

Loading Advanced Science Research Center collaborators
Loading Advanced Science Research Center collaborators