Study offers new target for antibiotic resistant bacteria

As antibiotic resistance rises, the search for new antibiotic strategies has become imperative. In 2013, the Centers for Disease Control estimated that antibiotic resistant bacteria cause at least 2 million infections and 23,000 deaths a year in the U.S.; a recent report raised the likely mortality rate to 162,044.
New Cornell research on an enzyme in bacteria essential to making DNA offers a new pathway for targeting pathogens. In “Convergent Allostery in Ribonucleotide Reductase,” published June 14 in Nature Communications, researchers used the MacCHESS research stations at the Cornell High Energy Synchrotron Source (CHESS) to reveal an unexpected mechanism of activation and inactivation in the protein ribonucleotide reductase (RNR).

Understanding the “switch” that turns RNR off provides a possible means to shut off the reproduction of harmful bacteria.
RNRs take ribonucleotides, the building blocks of RNA, and convert them to deoxyribonucleotides, the building blocks of DNA. In all organisms, the regulation of RNRs involves complex mechanisms, and for good reason: These mechanisms prevent errors and dangerous mutations.

>Read more on the CHESS website

Image: William Thomas, a graduate student in the field of chemistry and chemical biology, collects data on ribonucleotide reductase.

PREM students outfitting and upgrading CHESS x-ray beamlines

CHESS is fortunate to have three graduate students visiting from Puerto Rico. Supported by the NSF-PREM CiE2M – the Center for Interfacial Electrochemistry of Energy Materials – a partnership of The University of Puerto Rico, Rio PiedrasCampus (UPRRP), Universidad Metropolitana (UMET) and Universidad del Turabo (UT), and CHESS. 

This group forms an educational and innovative collaborative materials research effort to bring together a diverse and talented scientific community with experience and expertise in electro-chemistry, solid-state and inorganic chemistry, and synchrotron-based techniques to character energy materials in operando conditions at CHESS.  
The students have become an integral part of the team building out and commissioning new X-ray beamlines at the upgraded CHESS facility. New to them was learning good ultra-high vacuum (UHV) practices, using tools like torque wrenches to set vacuum seals, and using an RGA to find chemical contamination in optics boxes (“was really interesting!”). They have also studied the design of beamline components in each sector: apertures, safety bricks and power filters required to deliver X-rays to experimental hutches.
Melissa’s favorite activity was assembling components for Sector 4 X-ray monochromator. “It is like a puzzle to solve. There are many different plates and bolts and it is a real challenge to assemble based on the 3D CADmodel. There is a correct order to do things. It was fun to install water cooled components in the vacuum chamber,” she says.

>Read more on the CHESS website

Image: Brenda, Joesene, Melissa, and Alan Pauling (right) of CHESS proudly display their ultra-high vacuum assembly and installation in the Sector 2 cave of the new CHESS beamline. The students have worked hand-in-hand with CHESS staff to assemble, test and prepare the X-ray beampipes in three different sectors of CHESS. 

Biofortification of field-grown cassava

Micronutrient deficiency, sometimes called the “hidden hunger,” causes severe health problems in hundreds of millions of people worldwide, and is particularly damaging to children, in whom it can impair both physical and cognitive development.

Biofortification is one of the most promising tools available for alleviating this problem, but is a multifaceted challenge involving not only creating nutrient-rich crop varieties, but also ensuring bioavailability of these nutrients, protecting against increased uptake of toxins such as cadmium, and adoption by affected populations.

Image: X-ray Fluorescence images, obtained at CHESS, comparing localization of Fe, Zn, and Ca in the stems and storage roots of several genetically distinct varieties of Cassava; (from Narayanan et al, doi: 10.1038/s41587-018-0002-1). Scale bars: 1 mm.

Intermittent plasticity in individual grains

A study using high energy x-ray diffraction.

Understanding the behavior of metals undergoing deformation is critical to design for fuel efficiency, performance and safety/crashworthiness. Traditional engineering analysis treats metal deformation as a smooth motion, like a fluid, when in reality the flow is intermittent at finer length scales. Use of a new detector enabled the study of these intermittent bursts of deformation at the scale of individual crystals in a loaded test sample.
A metal component is polycrystalline, composed of many crystals or grains. At the scale of millimeters, the deformation of a metal appears to proceed smoothly, whereas at the microscopic scale the underlying processes occurring in individual grains proceed in fits and starts. In this collaboration between researchers at Cornell University, the University of Illinois at Urbana-Champaign, the Air Force Research Laboratory and the Advanced Photon Source of Argonne National Laboratory, a high-speed detector was used to study these microscale deformation bursts in a grain-by-grain manner.

>Read more on the CHESS website

Image: The MM-PAD is shown with the vacuum cover and x-ray window removed. The 2×3 arrangement of detector modules are the brownish squares in the center.  Each module consists of 128×128 square pixels, where each pixel is 150µm of a side. Each module is roughly 2 cm x 2 cm in size. There is a 5 pixel wide (0.75 mm) inactive area between adjacent modules. (This photo is of an MM-PAD with Si, instead of CdTe sensors; otherwise, the two types of MM-PADs look identical.)

Conclusion of the construction project: CHESS-U.

Fourteen months ago, Lt. Gov. Kathy Hochul came to the Cornell High Energy Synchrotron Source (CHESS) to announce a $15 million grant from the New York State Upstate Revitalization Initiative.

The URI funding was for an upgrade project – dubbed “CHESS-U” – which would arm CHESS with enhanced X-ray capabilities, keeping it a leading synchrotron source in the U.S. The project was also expected to create dozens of jobs, both at Cornell and across the region.
On Jan. 17, Hochul returned to Wilson Laboratory, the home of CHESS, to proclaim the project complete in an event that drew local lawmakers, stakeholders from Cornell, and representatives from several local and regional manufacturers whose contributions were on display during a short tour of the new experiment hutches and other equipment.
There is still some work to be done related to the project, and the linear accelerator and synchrotron beams – which were turned off for CHESS-U on June 4, 2018 – aren’t scheduled to be turned back on until Jan. 23. The event marked the official end of the construction project, for which crews worked double shifts over the final six months of 2018 in order to minimize downtime. In addition, wall and ceiling segments for most of the new experiment hutches were built off-sight at Advanced Design Consulting of Lansing and shipped to CHESS for installation. Beamlines will gradually be recommissioned in the coming months.

>Read more on the CHESS website

Image: CHESS Director Joel Brock, left, takes Lt. Gov. Kathy Hochul on a tour of the new construction at the Cornell High Energy Synchrotron Source during an event Jan. 17 to mark the conclusion of the $15 million upgrade project, known as CHESS-U.
Credit:

50 years later, Wilson Lab stays cutting edge

October 2018 marks the 50th anniversary of the dedication of the Wilson Synchrotron Laboratory.

Initially built for $11million and promising to deliver cutting-edge research in elementary particle physics, it was the NSF’s largest project at that time. Fifty years later, the lab is going through its biggest upgrade in decades.
Chris Conolly looks at the concrete floor of Wilson Lab, eyeing up the numerous holes drilled by one of the contractors for the upgrade project. These one-inch holes pockmark the 10,000sf experimental hall of the Wilson Synchrotron Laboratory. In a way, these holes represent the numerous experiments conducted over the past 50 years.

There are a lot of holes. 652 to be exact, as the CHESS X-ray Technical Director and CHESS-U beamline project manager easily points out.
“It’s almost like being an archaeologist”, says Conolly, as he walks through the maze of newly constructed hutches in the experimental hall. He stops near the sector II hutches, “especially this spot here,” he says, presenting a repeating pattern of drilled holes arcing across the floor. The pattern spans a total of about 25 feet, and Chris, who has been with CHESS for the past 18 years, has no idea what was held down by the bolts marked in the floor.

>Read more on the Cornell High Energy Synchrotron Source website

Image: Robert Wilson, right, was the architect behind Wilson Lab, as well as many of the subsequent experiments. Wilson later went over to Fermilab to design their famed building. 

Defense spending bill extends Air Force research partnership

For the past 10 years, the U.S. Air Force has funded research on high-performance materials at the Cornell High Energy Synchrotron Source (CHESS).

The partnership has resulted in numerous advances, including a greater understanding of metal fatigue and analysis of the best metals for aircraft.
This partnership was extended with $8 million in funding to CHESS as part of the fiscal year 2019 defense appropriations bill, a $674.4 billion package that President Donald Trump signed into law Oct. 1. The bill passed both the U.S. Senate – supported by New York Sens. Charles Schumer, who is Senate minority leader, and Kirsten Gillibrand – and the U.S. House of Representatives late last month.

“Cornell University is deeply grateful to Leader Schumer and Senator Gillibrand for securing $8 million in additional funding for CHESS,” Cornell President Martha E. Pollack said in a statement. “Maintaining our scientific infrastructure is essential if the U.S. is to keep its competitive advantage in research and development. Over the years, taxpayers have invested more than $1 billion in CHESS, an investment that’s paid off many times over in new discoveries, breakthrough technologies, [science, technology, engineering, math] education and workforce development.”

Image: Matthew Miller, right, associate director of the Cornell High Energy Synchrotron Source (CHESS), watches graduate student Mark Obstalecki prepare a sample for analysis in the F2 hutch at CHESS.

New hutches installed as CHESS-U takes shape

The construction portion of the CHESS-U upgrade is nearing completion as teams work to assemble the last of the experimental hutches. While there is still plenty of work to be done, the preparation for becoming a true 3rd-generation lightsource is paying off.

In early 2019, CHESS-U will have an increased energy of the electron beam, from 5.3 to 6.0 GeV, double the current from 100 to 200 mA, and reduction of the horizontal emittance of the x-ray beam from 100nm to 30nm.
While these high energy x-rays will soon benefit researchers from around the world, new hutches are currently being built to contain and control the beam from the new undulator sources being installed. These hutches, or light-tight experimental rooms, will contain the x-rays by using multiple layers of lead for the walls and ceilings with additional shielding at the seams.

The design and installation of these hutches has been carefully coordinated. As utilities, cables and HVAC systems start to enter each room, it is worth noting the clever design that was used in order to retain the radiation-tight rooms. While safety was definitely at the forefront of the engineers’ minds, the ability to streamline the installation process was deliberately considered, and has since proven useful to compensate for any unavoidable delays.

>Read more on the CHESS website

Image: Kurt McDonald, CHESS Operator, helps install a new hutch for Sector 2. The modular design of the hutches has allowed for quicker installation. 

 

Microfluidic mixing chips can reveal how biomolecules interact

Christopher Flynn, a fourth year student majoring in Physics and Mathematics at Fort Lewis College, and a SUnRiSE student at Cornell this summer, is contributing to the design of microfluidic mixing chips which could significantly enhance our understanding of proteins and living cells.

Microfluidic mixing chips are used by scientists to analyze biological molecules. They have small channels in which biological solutions, usually solutions of protein, are mixed. Biological small angle x-ray solution scattering (BioSAXS) is then used to study how these biomolecules change under different conditions, for example when they mix with hormones and drugs or when they interact with other biomolecules. These observations can help further our understanding of how cells function.

With the intention of opening a door to the inner workings of cells, Flynn and Gillilan are continuing the work of Gillilan’s former postdoctoral student, Jesse Hopkins, who started a project on microfluidic chips more than two years ago. Hopkins was working on fabricating chips that could be used to observe molecular interactions and structural changes on a millisecond scale.

While Hopkins successfully designed almost every aspect of the chip, he was unable to get the final x-ray transparent window fixed on the chip without it leaking. Flynn’s main task over the summer is to resolve this. He creates chips in the Cornell NanoScale Science and Technology Facility (CNF), using techniques including photolithography and lamination. The chips have different layers, the faulty transparent window being in one of the last. After the first few layers of the chips are made, Flynn uses them to investigate different possibilities for the window. He expects to test these windows by pumping liquids through the chips, and if they have been fit successfully, to compare any results to computer simulations that Hopkins had developed.

>Read more on the Cornell High Energy Synchrotron Source

Image: Richard Gillilan and Topher Flynn. The channels of the mixing chips are 30 microns wide, 500 microns deep.; a difficult feat but important feature of the chip. 

The impact of summer undergraduate research programs extends beyond the laboratory

Conducting research at a world class facility is no doubt a once-in-a-lifetime experience for any undergraduate student.

By combining that research experience with meaningful peer-learning opportunities and dynamic outreach activities, a memorable summer of science inevitably occurs.
Summer undergraduate research students at CLASSE have been actively influencing the sphere of science education across campus and the community. During their brief time at CLASSE, these students are shaping the research that occurs in laboratory spaces, showcasing their efforts and understanding in conference rooms, and driving the conversations and questions that occur in communal areas. In the laboratory, student devote hours of their time combing through the literature, contributing to the investigation, collecting data, and compiling their results. In their offices, meeting rooms, and communal spaces students reveal their ideas, grow their understanding, and search for connections as they interact with their peers and network of mentors. In addition, outside of the lab and throughout campus and the greater community, students interact directly the public and share their passion for science.

Through informal presentations to mentors and colleagues, summer students reveal their insights and uncertainties surrounding their assigned projects. These talks provide young scientists and engineers with the opportunity to communicate their own understanding of their work to others. This communication helps to solidify their own understanding and stretch their abilities to express this knowledge in a clear, digestible manner.  Researchers must be skilled at transmitting their message so that others recognize the value and implications of their work. In order to be an effective scientist, students must practice being effective communicators and conveyors of knowledge for public consumption.

>Read more on the CHESS website

Image: Students provide others with updates on their research progress via informal chalk talks.

The machinist: A maker finds his calling in upstate New York

Join John Buettler, a machinist, as he shares the passion he brings to the job of helping to construct the Cornell High Energy Synchrotron Source (CHESS). CHESS is a high-intensity X-ray source, primarily supported by the National Science Foundation, that provides users with state-of-the-art synchrotron radiation facilities for research in physics, chemistry, biology and environmental and materials sciences.
Provided by Cornell University
Runtime: 3:41 

Synchrotron researchers uncover lost images from the 19th century

Art curators will be able to recover images on daguerreotypes, the earliest form of photography that used silver plates, after scientists learned how to use light to see through degradation that has occurred over time.

Research published today in Scientific Reports includes two images from the National Gallery of Canada’s photography research unit that show photographs that were taken, perhaps as early as 1850, but were no longer visible because of tarnish and other damage. The retrieved images, one of a woman and the other of a man, were beyond recognition. “It’s somewhat haunting because they are anonymous and yet it is striking at the same time,” said Madalena Kozachuk, a PhD student in the Department of Chemistry at Western University and lead author of the scientific paper.

“The image is totally unexpected because you don’t see it on the plate at all. It’s hidden behind time. But then we see it and we can see such fine details: the eyes, the folds of the clothing, the detailed embroidered patterns of the table cloth.”
The identities of the woman and the man are not known. It’s possible that the plates were produced in the United States, but they could be from Europe.
For the past three years, Kozachuk and an interdisciplinary team of scientists have been exploring how to use synchrotron technology to learn more about chemical changes that damage daguerreotypes.

>Read more on the Canadian Light Source (CLS) website

Image: A mounted daguerreotype resting on the outside of the vacuum chamber within the SXRMB (a beamline at CLS) hutch.
Credit: Madalena Kozachuk.

New technique simplifies creation of nanoparticle ‘magic-sized clusters’

One of the cool things about nanoparticles is also what makes them so difficult to work with: the fact that their properties are dependent on their size.

A critical challenge in translating nanomaterials from the laboratory into commercial applications, such as lighting or optical memory storage, is making a batch of nanoparticles all the same size. Two Cornell research groups have joined forces to lay out a solution for this issue.

Researchers in the labs of Richard Robinson and Tobias Hanrath – using X-ray analysis at the Cornell High Energy Synchrotron Source (CHESS) – have developed a new nanosynthetic pathway to achieve ultra-pure and highly stable groups of same-sized particles – known as “magic-sized clusters.”

Their paper, “Mesophase Formation Stabilizes High-Purity Magic-Sized Clusters,” published online Jan. 27 in the Journal of the American Chemical Society, and will be on a cover of the March 14 print edition. Lead authors are Curtis Williamson, doctoral student in both the Robinson and Hanrath groups, and Douglas Nevers, doctoral student in the Hanrath Group. Lena Kourkoutis, assistant professor of applied and engineering physics, also contributed.

>Read more on the Cornell Hight Energy Synchrotron Source (CHESS) website

Image: Schematic of the magic-sized clusters hexagonal mesophase. The mesophase (left) is an assembly of nanofibers (center), which are composed of magic-sized clusters (right).
Credit: Richard Robinson

A comparison of the etch mechanisms of germanium and silicon

Time multiplexed, deep reactive ion etching (DRIE) is a standard silicon microfabrication technique for fabricating MEMS sensors, actuators, and more recently in CMOS development for 2.5D and 3D memory devices.

At CHESS, we have adopted this microfabrication technique to develop novel x-ray optics called,Collimating Channel Arrays  (CCAs) [1], for confocal x-ray fluorescence microscopy (CXRF). Because the first CCA optics were fabricated from silicon substrates, the range of x-ray fluorescence energies for which they could be used, and hence the elements they could be used to study, was limited. Unwanted x-rays above about 11 keV could penetrate through the silicon, showing up as background and interfering with the measurement.

To solve the background problem, germanium substrates were used to fabricate the CCA optics. Germanium, which is much denser and therefore x-ray opaque than silicon, is also etch compatible with the fluorine etch chemistry for silicon DRIE. However, small differences in etch behavior between germanium and silicon can cause big differences in the outcome. Here, Genova et al JVST B [2] report a systematic comparison of  the etch mechanisms of silicon and germanium, performed with the Plasma Therm Versaline deep silicon etcher at the Cornell NanoScale Science & Technology Facility (CNF). The etch rates of silicon and germanium were compared by varying critical parameters in the DRIE process, especially the applied power and voltage used for each of 3 steps in the etch process,  on custom-designed wafers with a variety of features with systematically varying dimensions.

>Read more on the CHESS website

Image: (extract, full image here) SEM of high aspect ratio (>13:1) etched features in Si at 3.7 μm/min (a) and Ge at 3.4 μm/min (b)

X-ray detector for studying characteristics of materials

Sol M. Gruner’s group, Physics, has been a leader in the development of x-ray detectors for scientific synchrotron applications, and the team’s technology is used around the world. Their detectors utilize pixelated integrated circuit silicon layers to absorb x-rays to produce electrical signals. The wide dynamic range, high sensitivity, and rapid image frame rate of the detectors enable many time-resolved x-ray experiments that have been difficult to perform until now.

The detectors are limited by the silicon layer. Low atomic number materials such as silicon become increasingly transparent to x-rays as the energy of the x-rays rises. Gruner’s group is now developing a variant of their detector that will use semiconductors comprised of high atomic weight elements to absorb the x-rays and produce the resultant electrical signals. The Detector Group, led by Antonio Miceli, at the United States Department of Energy’s Advanced Photon Source (APS) will simultaneously develop the ancillary electronics and interfacing required to produce fully functional prototypes suitable for high x-ray energy experiments at the APS and CHESS.

>Read more on the CHESS website

Image: Sol M. Gruner, Physics, College of Arts and Sciences
Credit: Jesse Winter

 

Notes from the NSF INCLUDES Summit

Broadening the participation of underrepresented populations

For the past 20+ years, the National Science Foundation has been funding initiatives aimed at broadening the participation of underrepresented populations though the Broader Impact efforts supported by the various research divisions.

Millions of dollars and countless hours of work have done little to “move the needle” towards the desired outcome of achieving the full participation of diverse individuals in all facets of STEM. According to Dr. Alicia Knoedler who serves on NSF’s Committee on Equal Opportunities in Science and Engineering (CEOSE), states that the “cumulative, overall impact on underrepresented groups is minimal.”  To address this shortcoming, CEOSE released a list of recommendations to the NSF in their 2011-2012 report to implement a bold new initiative to fund broadening participation through institutional transformation and systems change using clear benchmarks of success, longitudinal data, and significant financial support. NSF Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science (INCLUDES) is what emerged from this report, along with adoption of a framework to ensure shared accountability to promote participation and excellence.

>Read more on the CHESS website

Image caption: Visual display depicting one brain-storming session held by NSF INCLUDES participants during the Summit held January 8-10th, 2018.