Annual Newsletter

 Ndiif Newsletter

This newsletter summarizes current capabilities and highlights usage trends to date for 2020. The NDIIF operates as a recharge facility and revises user fees every July 1.

Questions about NDIIF policies should be directed to the Director or any member of the steering committee. For technical and scheduling questions, see the relevant NDIIF staff members listed throughout the website. 

Sincerely

Professor Bradley Smith, Director of NDIIF

Fall 2020

NDIIF News Brief
  1. Electron Microscopy and Optical Microscopy Hire New Program Directors: Maksym Zhukovskyi is the new TEM Program Director of the Advanced Electron Microscopy Core. Sara Cole is the new Program Director of the Optical Microscopy Core.  Both of these new team members are instrumental in the day-to-day operations of the facility and also are available for protocol development, maintenance, usage, training, and all other general inquiries.  Please help us to welcome them to the NDIIF team!
  2. NDIIF Awards for Best Imaging Publications in 2019: 
      • The Best Electron Microscopy Imaging Publication Award for 2019 was awarded to Spencer Golze, a graduate student with Professor Svetlana Neretina in the Department of Aerospace and Mechanical Engineering.
      • The Best Biological Imaging Publication Award for 2019 was awarded to Cynthia Spires, a graduate student with Professor Bradley Smith in the Department of Chemistry and Biochemistry. 
      • The Best Artisitc Image Award for 2019 was awarded to Brooke Chambers, a graduate student with Professor Rebecca Wingert in the Department of Biological Sciences.
    • Image submission for Best Imaging Publication Award in 2020 is open now and will end mid-March, 2021. 
  3. CTSI Core Facility: Affiliation with CTSI as a core research facility was renewed. For more information please visit:  http://www.indianactsi.org

Funding opportunity and grants are continually available through CTSI.  Please inquire for further information.  NDIIF staff is available to assist in budget preparation and to develop scope of work.

  1. Advanced Electron Microscopy Core: new cryo-TEM equipment was purchased. A Leica Automatic Plunge Freezer EM GP2 and Leica EM UC7 ultramicrotome equipped with the FC7 cryo chamber attachment is now located in room B16.  Samples can be imaged on the JEOL 2011 using a JEOL single tilt holder for room temperature bio specimens imaging and a Fishione 2550 cryo transfer holder for imaging frozen-hydrated/vitrified bio specimens. (At cryo condition TEM imaging is limited to 20,000 magnification).
  2. Optical Microscopy Core: a new image analysis software was purchased.  IMARIS is a widely used tool for multiple facets of data analysis within the field of microscopy and can be used as a remote tool for users located on and off the Notre Dame campus.

Established in 2008, the NDIIF provides an integrated suite of sophisticated microscopes and imaging stations that enable the expert users to attack the most complex modern research problems and, equally important, the resident professional staff (technicians and research specialists) to guide the non-expert users

 

Advanced Microscopy                  Optical Microscopy                         Histology                             InVivo Imaging

Feature Stories

Fabrication of suspended antenna-coupled nanothermocouples

Gergo P. Szakmany, Alexei O. Orlov, Gary H. Bernstein, and Wolfgang Porod

Citation: Journal of Vacuum Science & Technology B37, 052201 (2019); doi: 10.1116/1.5113506


Here we highlight a series of SEM images taken by the Magellan SEM and the Helios FIB about suspended antenna-coupled nanothermocouples(ACNTCs). These devices are far-infrared detectors, and their operation is based on the wave nature of the IR radiation. A nanowire antenna, tuned for IR wavelength, is resonantly absorbs the incident IR radiation and heat the hot junction of the thermocouple. The voltage generated by the nanothermocouple is proportional to the incident radiation energy. Fabricating these devices above a cavity etched into the Si substrate increased their response about 100 times. The first publication (Scientific Reports)shows the main results, and the second publication (JVST) shows the fabrication details. The imaging tools at the Electron Microscopy core of NDIIF helped us to understand the initial failures of the devices. Specifically, the high resolution SEM images allowed us to see any residues under the antennas after the cavity etch that was responsible to the braking of the devices. In addition, the antenna response depends on the cavity, the FIB allowed us to precisely measure the depth of the cavity. We used these data to simulate our devices with COMSOL, and to support our experimental results with numerical simulations.The growth mechanisms and defect formation in Au seeds and nanoplates have been studied based on SEM and TEM analysis. A combination of High Resolution TEM and STEM imaging as well as Selected Area Electron Diffraction (SAED) performed using an FEI Titan 80-300. TEM has been employed for structural and compositional characterization of the samples. TEM cross-sectional samples were prepared using an FEI Helios SEM/FIB dual beam tool. The cross-sectional TEM images provide evidence that Au seeds and the hexagonal nanoplates contain planar defects, twins, and stacking faults, that are parallel to the substrate surface. The presence of twins in the seeds and nanoplates is also evidenced by the corresponding electron diffraction pattern.

This manuscript investigated the penetration of a copper-catalyzed azide–alkyne cycloaddition click reactive solution within a nanofiltration membrane. The need from this work was to develop a method for monitoring a diffusion controlled reaction, in which a reactive solution is placed upon the surface of a copolymer membrane and let to diffuse into the membrane at short time intervals. The progress of the reaction was quantified by scanning electron microscopy with energy dispersive x-ray spectroscopy to visualize the progression of the reactive front. From the membrane cross-section. Using a reactive solution containing propargyl chloride, the progression of the coupling reaction could be monitored by the visualization of chlorine atoms via EDX mapping. The reaction was performed for 0, 60, 120, and 300 secs, with the resulting chlorine intensity increasing within the depth of the membrane as the exposure time increased. Additionally, multiple reactions were sequenced to react surface and short depth level azides with propargylamine, and then converting the underlying azides with chloride. These EDX images showed that the initial reaction fully reacted the azide moieties, shown by no chlorine detection, with high detection seen underneath. This confirmed this reaction pathway is capable of controlling the membrane functionalization process. 

Gergo Szakmany Jvst Gergo Szakmany



 

 

 

 

Cavity Backed Antenna-Coupled Nanothermocouples

Gergo P. Szakmany , Alexei O. Orlov, Gary H. Bernstein & Wolfgang Porod. ScientificRepoRts | (2019) 9:9606 | https://doi.org/10.1038/s41598-019-46072-4

This paper reports a two-orders-of-magnitude improvement in the sensitivity of antenna-coupled nanothermocouple (ACNTC) infrared detectors. The electrical signal generated by on-chip ACNTCs results from the temperature difference between a resonant antenna locally heated by infrared radiation and the substrate. A cavity etched under the antenna provides two benefits. It eliminates the undesirable cooling of the hot junction by thermally isolating the antenna from the substrate. More importantly, careful cavity design results in constructive interference of the incident radiation reflected back to the antenna, which significantly increases the detector sensitivity. We present the cavity-depth-dependent response of ACNTCs with cavity depths between 1 μm and 22 μm. When constructive interference is maximized, the thermal response increases by 100-fold compared to devices without the cavity.

Gergo Szakmany Scientificreports Gergo Szakmany


 

 

 

 


 

 

Controlled Post assembly Functionalization of Mesoporous Copolymer Membranes Informed by Fourier Transform Infrared Spectroscopy

JohnR.Hoffman, AndrewD.Mikes, FengGao, andWilliamA.Phillip

ACS Applied Polymer Materials. 2019 1 (8), 2120-2130

DOI: 10.1021/acsapm.9b00419

This manuscript investigated the penetration of a copper-catalyzed azide–alkyne cycloaddition click reactive solution within a nanofiltration membrane. The need from this work was to develop a method for monitoring a diffusion controlled reaction, in which a reactive solution is placed upon the surface of a copolymer membrane and let to diffuse into the membrane at short time intervals. The progress of the reaction was quantified by scanning electron microscopy with energy dispersive x-ray spectroscopy to visualize the progression of the reactive front. From the membrane cross-section. Using a reactive solution containing propargyl chloride, the progression of the coupling reaction could be monitored by the visualization of chlorine atoms via EDX mapping. The reaction was performed for 0, 60, 120, and 300 secs, with the resulting chlorine intensity increasing within the depth of the membrane as the exposure time increased. Additionally, multiple reactions were sequenced to react surface and short depth level azides with propargylamine, and then converting the underlying azides with chloride. These EDX images showed that the initial reaction fully reacted the azide moieties, shown by no chlorine detection, with high detection seen underneath. This confirmed this reaction pathway is capable of controlling the membrane functionalization process.

John Hoffman Ndiif Slide John Hoffman 1 1024 1

 

 

 

Slt, MltD, and MltG ofPseudomonas aeruginosaas Targets ofBulgecin A in Potentiation ofβ‑Lactam Antibiotics

David A. Dik, Chinedu S. Madukoma, Shusuke Tomoshige, Choonkeun Kim, Elena Lastochkin, William C. Boggess, Jed F. Fisher, Joshua D. Shrout, and Shahriar Mobashery

ACS Chemical Biology 2019 14 (2), 296-303 DOI: 10.1021/acschembio.8b01025

The interplay between the activities of lytic transglycosylases (LTs) and penicillin-binding proteins (PBPs) is critical for the health of the bacterial cell wall. Bulgecin A (a natural-product inhibitor of LTs) potentiates the activity of β-lactam antibiotics (inhibitors of PBPs), underscoring this intimate mechanistic interdependence. Bulgecin A in the presence of an appropriate β-lactam causes bulge deformation due to the formation of aberrant peptidoglycan at the division site of the bacterium. AsPseudomonas aeruginosa, anefarious human pathogen, has 11 LT paralogs, the answer as to which LT activity correlates with β-lactam potentiation is important and is currently unknown. Growth ofP. aeruginosaPAO1 strains harboring individual transposon-insertion mutants at each of the 11 genes forLTs, in the presence of theβ-lactam antibiotic ceftazidime or meropenem, implicated the gene products of slt,mltD, andmltG(of the 11), in bulge formation and potentiation. Hence, the respective enzymes would be the targets of inhibition by bulgecinA, which was indeed documented. We further demonstrated by imaging in real time and by SEM that cell lysis occurs by the structural failure of this bulge. Upon removal of theβ-lactam antibiotic prior to lysis,P. aeruginosa experiences delayed recovery from the elongation and bulge phenotype in the presence of bulgecin A. These observations argue for a collaborative role for the target LTs in the repair of the aberrant cell wall, the absence of activities of which in the presence of bulgecin A results in potentiation of theβ-lactam antibiotic. 

Ddik 2019 Em

 


 

 

 


 

 

Quantification of Multiple Mixed Contrast and Tissue Compositions Using Photon-Counting Spectral Computed Tomorgraphy

Tyler E. Curtis and Ryan K. Roeder

Journal of Medical Imaging 6(1), 013501 (Jan–Mar 2019)

Computed tomography (CT) is the most widely used clinical diagnostic imaging modality but is only suitable for anatomic imaging, e.g., discriminating bone vs. soft tissue or a contrast agent vs. normal tissue. Photon-counting spectral CT is a nascent imaging technology that promises to be transformative by enabling molecular imaging with CT. Tyler’s paper is significant because he demonstrated, for the first time, imaging capabilities with photon-counting spectral CT that are not possible with current clinical molecular imaging modalities –including nuclear imaging and magnetic resonance imaging. Using the MARS Bioimaging spectral CT system (MARS-12) located in the NDIIF In Vivo imaging facility and his own computer code for quantitative material decomposition, Tyler showed that multiple mixed (viz., spatially coincident within the same voxel) contrast agent (gadolinium, iodine) and tissue (calcium, water) compositions were able to be identified and quantified with high accuracy. We submitted this work to JMI, a relatively new and rising SPIE journal in the area of imaging physics, at the request of a editor who saw Tyler’s work presented at a conference. Finally, I would be remiss if I did not point out that Tyler overcame many challenges endemic to prototype systems in order to achieve these results. 

2019 Curtis Jmi Ryan Roeder