ACERT ANNOUNCES 2018 WORKSHOP ON REVOLUTIONARY NEW DENOISING METHODS
Conducting workshops on various aspects of ESR spectroscopy, both theoretical and experimental, has always been an important part of ACERT’s commitment to offer modern ESR technology to the wider biomedical community. At ACERT we are excited by the revolutionary new denoising methods we have introduced into the processing of ESR spectra, both cw and time domain. These wavelet-based denoising methods, outlined in our publications (1,2), have led to decreases in the data-acquisition time required for ESR data of one to two orders of magnitude; and our associated SVD (singular value decomposition)-based method for determining distance distributions in ESR data, as outlined in publication 3, has likewise allowed researchers to see multiple conformations that hitherto were hidden due to noise and poor resolution from previously-available regularization methods. To this end, in our next workshop we plan to provide training in this new technology to the ESR community.
The workshop will take place at ACERT on July 30-31, 2018, immediately following the large Rocky Mountain ESR conference so as to simplify travel concerns for conference attendees, especially those coming from Europe. Since this is a technology that has been developed at ACERT, the instructional lectures will be given by the key ACERT personnel. However, since many groups have begun to benefit from the methods as we process their data here, some of our collaborators will illustrate the power of the methodology for their varying biomedical studies, which include pulsed and cw ESR data as well as imaging data. All participants will be encouraged to bring raw data sets from their labs to be processed during the course of the workshop.
Details of the workshop will follow in the coming weeks.
1. M. Srivastava, C.L. Anderson, and J.H. Freed. "A New Wavelet Denoising Method for Selecting Decomposition Levels and Noise Thresholds" IEEE Access 4, 3862-3877 (2016). (Link: PDF)
2. M. Srivastava, E.R. Georgieva, and J.H. Freed. "A New Wavelet Denoising Method for Experimental Time-Domain Signals: Pulsed Dipolar Electron Spin Resonance" J. Phys. Chem. A 121, 2452-2465 (2017). (Links: PDF, Supplement)
3. M. Srivastava and J. H. Freed. "Singular Value Decomposition Method to Determine Distance Distributions in Pulsed Dipolar Electron Spin Resonance" J. Phys. Chem. Lett. 8, 5648-5655 (2017). (Links: PDF, Supplement)
September--New ACERT X/Q Pulsed ENDOR Spectrometer Facility.
In June, 2017, a state-of-the-art Bruker Elexsys-II E580 X/Q-Band pulsed Electron-Nuclear Double Resonance (ENDOR) ESR spectrometer was installed at the NIH P41-funded National Biomedical Center for Advanced ESR Technology (ACERT) at Cornell University, housed in the Department of Chemistry and Chemical Biology. Research groups at Cornell, the University of Rochester, SUNY Buffalo, and other future collaborating institutions can now use this modern commercial instrument. ACERT possesses the necessary expertise and technical capability to maintain the facility, which is unique in the Northeastern US.
ACERT, since its establishment in 2001, provides EPR expertise and service to many research groups nationally, which represent many biomedical fields. While the EPR currently performed in ACERT has been crucial in obtaining structural and functional information on paramagnetic cofactors in biological systems such as iron sulfur clusters, copper active sites etc., additional studies using ENDOR were often necessary but not available at Cornell for such users. Having an ENDOR shared capability at Cornell housed in ACERT will dramatically improve the quality of research for the groups participating in this proposal, as well as others who interact with ACERT. Facility users will have direct control of their ENDOR measurements, which will become part of their daily research. Also, importantly, ENDOR and EPR studies can now be carried out at the same time on the same samples and under the same conditions. As described below in the projects of major/minor users, ENDOR and EPR (e.g. ESEEM) are complementary to each other in terms of revealing different aspects of interactions between the unpaired electron and nuclear spins present in biological systems under study.
There are currently five major user groups planning to use our proposed ENDOR spectrometer, as well as additional minor users. The NIH-supported research projects of the major users include: (1) ENDOR study of novel chemistry of a [4Fe-4S]-cluster containing radical enzyme in diphthamide biosynthesis; (2) ENDOR and Electron-Spin Echo Envelope Modulation (ESEEM) to probe the role of hydration in membrane fusion; (3) ENDOR spectroscopy studies of proteins that mediate signal transduction through redox and photochemistry; (4) mechanism of inhibition of ribonuclease reductase by anti-cancer drugs; and (5) structure and dynamics of porphysomes — new photosensitive agents in cancer therapy and drug delivery. Additional projects from minor users include: (6)structure and function of artificial hydrogenases; (7) nitrification of enzymes and electron transfer proteins; and (8) hydration at lipid surfaces. Given the growing interest in ENDOR we also anticipate additional users.
The ACERT Elexsys-II ENDOR system is user-friendly and suitable for multiple users with a range of spectrometer configuration requirements. The types of user-friendly operations available at ACERT allow a rapid feedback between the expression, design, or synthesis of the system of interest and the analysis of its detailed structural parameters. For this reason, it was deemed appropriate to establish a fast-throughput ENDOR capability at ACERT, motivated by an initial group of key biomedical investigators. The good resolution for ENDOR at Q-band is a very important advantage of the proposed system. At the higher fields associated with Q-band frequencies, orientational spectra are spread over an almost 4 times larger range of frequencies than at X-band. This increases the ENDOR experiment's sensitivity to and resolution of small structural changes, in turn improving the quality of results for important biological applications of ESR, such as the determination of structures and mechanisms of enzyme catalytic centers.
July--Prof. Jack H. Freed is named a Fellow of the IES (International Electron spin/paramagnetic resonance) Society at their July 23-28 Quebec City meeting.
A Fellowship of the Society may be conferred on individuals who have made influential and distinguished contributions to the practice of EPR (ESR) Spectroscopy and its welfare over a long period.
June--Prof. Jack H. Freed is awarded the Voevodsky Prize during the IXth Voevodsky conference in Novosibirsk, Russia, June 25-30.
The Voevodsky Prize is awarded once every two years, in the memory of Academician V. V. Voevodsky of the Institute of Chemical Kinetics and Combustion of the Siberian Branch of the Russian Academy of Sciences and the International Tomography Center. The Prize is awarded to Russian and foreign scientists, in turn, for outstanding contributions to the investigation of mechanisms of chemical reactions, structure and properties of active intermediates, and elementary reactions in photo- and radiation chemistry by radiospectroscopic methods.
Awarding of the Voevodsky Prize is based on a competition. Candidates are nominated by scientific institutes or by individual scientists. The final decision is made by an Award Committee, consisting of 7 members. Members of the Committee are selected by the Scientific Council of the Institute of Chemical Kinetics and Combustion and are renewed each five years. The Voevodsky Prize is presented either at the session of the Scientific Council of the Institute of Chemical Kinetics and Combustion or during the conference dedicated to the memory of V. V. Voevodsky. An Awardee is expected to participate in these meetings and deliver a lecture on his scientific work.
New Signal Denoising Method Developed at ACERT
Madhur Srivastava, a graduate research assistant at ACERT, has developed a powerful new method to reduce noise in experimental signals of the types used in biomedical imaging research. The method can greatly improve image resolution and has the potential to significantly shorten the time needed to obtain images, with the eventual goal of allowing applications that are not feasible today, such as magnetic resonance imaging (MRI) scans in emergency-room situations. While standard denoising methods can reduce random noise, not correlated with any signal, they do poorly with correlated noise that indicates the presence of data peaks. By splitting experimental signals into wavelets, different frequency components, his algorithm can find those peaks and then remove the correlated noise as well. To date, the new technique has been able to reduce data acquisition times by an order of magnitude or more. Two papers have been published with Madhur as lead author. The first paper, a general description of the algorithm, was published in July, 2016, in IEEE Access (available here); and the second, describing the algorithm's application to PDS ESR, was web-published in early March, 2017, in J. Phys. Chem. A (available here). In addition, a provisional patent (U.S. No. 62/334,626; filed May 11, 2016) has been obtained. Several other publications are in preparation.
Funding Awarded for ENDOR Spectrometer
In July, 2016, Cornell was awarded $1.4M by the National Institutes of Health (NIH) to purchase a Pulsed EPR/ENDOR Spectrometer System from the Bruker Biospin Corp. This instrument will allow us to establish the only center for Pulsed Electron-Nuclear Double Resonance (ENDOR) in the Northeast U.S. Multiple research groups at Cornell and elsewhere in NY will be principal users of the instrument. Professor Emeritus Jack H. Freed is the PI of this NIH grant, and the spectrometer will be located in ACERT and be maintained by ACERT personnel.
ACERT Graduate Student Selected for Engineering College Commercialization Fellows Group
In May, 2016, ACERT graduate research assistant Madhur Srivastava was one of six Ph.D. students selected to be the first group of Commercialization Fellows, a program in Cornell University's College of Engineering, created to give students opportunities to learn how to take their newly-developed technologies and turn them into potential businesses. Madhur has been researching a new method for denoising signals in ESR and other type of magnetic resonance techniques. The article appears in the Cornell Chronicle.
ACERT 2015 Workshop and Symposium
We are pleased to report that the latest ACERT Workshop, "Computational Methods in ESR", was once again well-attended and successful. This year, we brought together scientists and students for discussion of available software and simulation techniques related to ESR/EPR magnetic resonance.
ACERT featured in Biophysical TV video
Jack Freed receives 2014 ACS Joel Henry Hildebrand Award in the Theoretical and Experimental Chemistry of Liquids:
American Chemical Society announced that Jack H. Freed is the 2014 recipient of the Joel Henry Hildebrand Award in the Theoretical and Experimental Chemistry of Liquids sponsored by ExxonMobil Research and Engineering Co. The national award recognizes distinguished contributions to the understanding of the chemistry and physics of liquids. Professor Freed was presented the award at the Society’s 247th ACS National Meeting in Dallas, TX on Tuesday, March 18, 2014. He was invited to deliver an award talk. The talk was entitled “ESR Perspective on Complex Liquids (A Retrospective)”
An article reporting about Dr. Freed’s work and the award appeared the February 10 issue of Chemical & Engineering News (Vol. 92, Issue 6, p.31): http://cen.acs.org/articles/92/i6/Joel-Henry-Hildebrand-Award-Theoretical.html
Jack Freed awarded 2013 ISMAR Prize:
The ISMAR Prize is awarded every three years for outstanding achievement in the field of magnetic resonance.
Jack Freed’s work is honored: "For the foundation of modern EPR through an extraordinary range of contributions from mathematics and theory to methodology and instrumentation; and for the application of his ingenious methods of pulsed EPR spectroscopy to fundamental problems in areas from chemistry to biophysics."
"A Conversation with Jack H Freed" (Interview with Brian Crane)
"Study Reveals New Insights into the Function of Transporters in the Brain Implicated in Stroke and Neurodegenerative Disease"
Weill Cornell Newsroom, February 4, 2015.
"Chemists show that ALS is a protein aggregation disease"
by Anne Ju, Cornell Chronicle, October 20, 2010.
"A new spin on ESR"
by Michael Gross, Chemistry and Industry, August 2010.
by Michael Gross, Chemistry World, May 2010, pp. 50-53.