Annual Newsletter

 Ndiif Newsletter

This newsletter summarizes current capabilities and highlights usage trends to date for 2019. 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. 


Professor Bradley Smith, Director of NDIIF

Fall 2019

NDIIF News Brief
  1. Midwest Imaging and Microanalysis Workshop at Notre Dame: The sixth annual workshop, held May 2019, was very successful with a focus on electron beam technologies. Visitors were welcomed from various Universities and venues. 
  2. NDIIF Awards for Best Imaging Publications in 2018: 
      • The Best Electron Microscopy Imaging Publication Award for 2018 was awarded to Michael Brennan, a graduate student with Professor Masaru Kuno in the Department of Chemistry and Biochemistry.
      • The Best Biological Imaging Publication Award for 2018 was awarded to Yide Zhang, a graduate student with Scott Howard in the Department of Electrical Engineering. 
    • Image submission for Best Imaging Publication Award in 2019 is open now and will end mid-March, 2020. 
  3. CTSI Core Facility: Affiliation with CTSI as a core research facility was renewed. For more information please visit:

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: a new SEM/FIB workstation was purchased. The Helios G4 UX is a fully digital, Extreme High Resolution (XHR) Field Emission Scanning Electron Microscope (FE SEM) equipped with Focused Ion Beam (FIB) technology.
  2. Optical Microscopy Core: a Nikon CSU Spinning Disk System was purchased and is housed at Harper Cancer Research Institute under the management of the NDIIF.  This instrument is available for training and online reservations for imaging.

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

Effects of bisphosphonate ligands and PEGylation on targeted delivery of gold nanoparticles for contrast-enhanced radiographic detection of breast microcalcifications

Lisa E. Cole, Tracie L. McGinnity, Lisa E. Irimata, Tracy Vargo-Gogola, Ryan K. Roeder, Acta Biomaterialia 82 (2018) 122-132, DOI: 10.1016/j.actbio.2018.10.014

Imaging Significance: TEM (Titan) and SEM (Magellan) were used to verify consistency in the size distributions between groups and directly observe targeting, respectively. Radiographic contrast in mammary tissue was observed longitudinally in vivo after administration of AuNP imaging probes using micro-computed tomography (Albira). The biodistribution and cytocompatibility of AuNPs in various organs and tissues was characterized by optical microscopy of tissue sections (Histology core).

Scientific Significance: Gold nanoparticle (AuNP) imaging probes and therapeutics are commonly surface functionalized with PEG and/or targeting ligands. However, direct comparisons of PEGylated AuNPs with and without a targeting ligand, or ligand-targeted AuNPs with and without a PEG-spacer, are lacking in the literature. Therefore, this study was designed to directly compare the in vivo targeting efficiency, biodistribution, and clearance of PEGylated AuNPs with and without a bisphosphonate (BP) targeting ligand, and BP-targeted AuNPs with and without a PEG spacer, in a preclinical murine model of breast microcalcifications. The functional ligand and PEG-spacer were shown to be critical for in vivo targeting and clearance, respectively, using a breadth of NDIIF instrumentation.

Translational Significance: BP-PEG-AuNPs were shown to improve radiographic detection of microcalcifications associated with breast cancer in a model of dense breast tissue. Breast tissue density is known to compromise the accuracy of mammographic screening. 

Cole 2018














Super-resolution fluorescence microscopy by stepwise optical saturation

Yide Zhang, Prakash D. Nallathamby, Genevieve D. Vigil, Aamir A. Khan, Devon E. Mason, Joel D.Boerckel, Ryan K. Roeder, and Scott S. Howard. Vol. 9, No. 4 | 1 Apr 2018 | BIOMEDICAL OPTICS EXPRESS.

This paper demonstrates true super-resolution microscopy using the NDIIF’s conventional fluorescence microscopes. Super-resolution microscopy is a ground breaking technology that allows researchers to see features smaller than the diffraction limit of light. Many techniques have been developed and used to produce significant biological results, and the impact of super-resolution microscopy was recognized in the awarding of the 2014 Nobel Prize in Chemistry to the first pioneers in the eld. However, these techniques require expensive specialized equipment and can be limited to simple samples. This paper describes and demonstrates a method for achieving super-resolution imaging using commonly available microscopes in a way that allows for 3Dsuper-resolution imaging in scattering tissue. Super-resolution in this paper is accomplished through a new understanding of how focused light interacts with saturable fluorophores. This means that anyone currently using conventional scanning fluorescence microscopy can us the technique to improve their resolution. This is the first demonstration of the technique which subsequently has been used to achieve the first ever super-resolution frequency-domain fluorescence lifetime imaging microscopy and long-term, 3D in vivo imaging of zebra sh neurons during spinal chord formation.







Validation of Matrix Metalloproteinase‑9 (MMP-9) as a Novel Target for Treatment of Diabetic Foot Ulcers in Humans and Discovery of aPotent and Selective Small-Molecule MMP‑9 Inhibitor ThatAccelerates Healing

Trung T. Nguyen,†Derong Ding,†William R. Wolter,‡Rocio L. Pérez,†Matthew M. Champion,†Kiran V. Mahasenan,†Dusan Hesek,†Mijoon Lee,†Valerie A. Schroeder,‡Jeffrey I. Jones,†Elena Lastochkin,†Margaret K. Rose,†Charles E. Peterson,§Mark A. Suckow,‡,∥Shahriar Mobashery,†and Mayland Chang Kamat, J.Med.Chem.2018, 61, 8825−8837

Diabetic foot ulcers (DFUs) are a significant health problem. A single existing FDA-approved drug for this ailment, becaplermin, is not standard-of-care. We previously demonstrated that upregulation of active matrix metalloproteinase (MMP)-9 is the reason that the diabetic wound in mice is recalcitrant to healing and that MMP-8 participates in wound repair. In the present study, we validate the target MMP-9 by identifying and quantifying active MMP-8 and MMP-9 in human diabetic wounds using an affinity resin that binds exclusively to the active forms of MMPs coupled with proteomics. Furthermore, we synthesize and evaluate enantiomerically pure (R)- and (S)-ND-336, as inhibitors of the detrimental MMP-9, and show that the (R)-enantiomer has superior efficacy in wound healing over becaplermin. Our results reveal that the mechanisms of pathology and repair are similar in diabetic mice and diabetic humans and that (R)-ND-336 holds promise for the treatment of DFUs as a first-in-class therapeutic.  


Loughran 2018

 Aging Increases Susceptibility to Ovarian Cancer Metastasis in Murine Allograft Models and Alters Immune Composition of Peritoneal Adipose Tissue

Elizabeth A. Loughran*,†,‡, Annemarie K. Leonard*‡,Tyvette S. Hilliard*,‡, Ryan C. Phan‡,Madeleine G. Yemc‡, Elizabeth Harper*‡,Emma Sheedy‡, Yuliya Klymenko‡,§,Marwa Asem*,†,‡, Yueying Liu*,‡, Jing Yang*,‡,Jeff Johnson*,‡, Laura Tarwater , Zonggao Shi*,‡,Matthew Leevy‡,§, Matthew J. Ravosa‡,§,¶,#andM. Sharon Stack*,‡ Neoplasia Vol.20, No. xx, 2018.

Ovarian cancer is the deadliest gynecological malignancy in the US. Despite the fact that age is a significant risk factor for the development of ovarian cancer, there are little published data which address the impact of aging on ovarian cancer metastasis. In this study, we demonstrated that aged mice (>20 months) develop greater metastatic tumor burden than young mice when injected with syngeneic ovarian cancer cells. Live imaging was used to monitor tumor progression over the course of4 weeks in 28 mice. Not only does the submitted image (Figure 2A) provide an impressive visual of the difference in tumor burden between the young and aged cohorts, the longitudinal nature of this study is noteworthy when many tumor studies only image tumor burden at the endpoint. Our study entitled “Aging Increases Susceptibility to Ovarian Cancer Metastasis in Murine Allograft Models and Alters Immune Composition of Peritoneal Adipose Tissue” provides a strong foundation for future studies investigating the impact of age on metastasis. This is timely research as there is an aging global population and the number of older women diagnosed with OvCa is expected to rise.



GaN/NbN epitaxial semiconductor/ superconductor heterostructures

Yan 2018

Rusen Yan1*, Guru Khalsa2*, Suresh Vishwanath1, Yimo han3, John Wright2, Sergei rouvimov4, D. Scott Katzer5, Neeraj Nepal5, Brian P. Downey5, David a. muller3,6, huili G. Xing1,2,6, David J. meyer5 & Debdeep Jena1,2,6, Nature 555 (2018)183–189.

TEM provided the evidence of crystalline structure of novel epitaxial NbNx layers that appeared to be cubic, with high crystalline quality over large areas. Occasional twin boundaries were seen resulted from the presence of atomic steps on the substrate surface due to symmetry mismatch between cubic NbNx and hexagonal SiC and AlN . TEM evidenced that both AlN on the NbNx to be of nitrogen polarity; the entire AlN layer and all subsequent nitride semiconducting layers are hexagonal. The structure of the layers are of nigh importance because it effects the physical properties of the hetero-structures and performance of device that were fabricated on such novel heterostructures. This project was one of many joint projects with Cornell university showing a high interest of our collaborators to NDIIF facility and high level expertise at UND.




Brennan Ndiif Imaging Award Slides Michael Brennan

 Crystal Structure of Individual CsPbBr3Perovskite Nanocubes 

Michael C. Brennan,*,†Masaru Kuno,†,‡and Sergei Rouvimov*,§ Inorganic Chemistry 2019 58 (2), 1555-1560 DOI: 10.1021/acs.inorgchem.8b03078C6TB01659F

The exact crystal structure assumed by CsPbBr3 nanocubes (NCs) remains ambiguous, whether cubic or orthorhombic. Here the atomic structure of individual CsPbBr3 NCs is considered via high-resolution transmission electron microscopy (HRTEM) defocus-series analyses. The technique entails acquiring lattice-resolved HRTEM images of individual NCs over progressive defocus values. CsPbBr3 NC atomic structure was evaluated by comparing acquired experimental data to simulated lattice-resolved images and corresponding Fourier transform patterns of both orthorhombic (Pnma) and cubic (Pm3̅m) CsPbBr3 polymorphs. The analyses indicate that both polymorphs exist simultaneously for NCs with 10 nm edge lengths. When edge lengths are <5 nm,however, only cubic symmetry is observed signifying a potential size dependence to the crystal symmetry of CsPbBr3 NCs. Such structural measurements provide critical insight into elucidating the structure/(optical and electrical) function relationship of CsPbBr3 NCs. 


Dik 2018

 Total Syntheses of Bulgecins A, B, and C and Their Bactericidal Potentiation of the β‑Lactam Antibiotics

Shusuke Tomoshige,† David A. Dik,† Masaaki Akabane-Nakata,† Chinedu S. Madukoma,‡ Jed F. Fisher,† Joshua D. Shrout,‡,¶ and Shahriar Mobashery*,† ACS Infect. Dis. 2018, 4, 860−86

The bulgecins are iminosaccharide secondary metabolites of the Gram-negative bacterium Paraburkholderia acidophila and inhibitors of lytic transglycosylases of bacterial cell-wall biosynthesis and remodeling. The activities of the bulgecins are intimately intertwined with the mechanism of a cobiosynthesized β-lactam antibiotic. β-Lactams inhibit the penicillin-binding proteins, enzymes also critical to cell-wall biosynthesis. The simultaneous loss of the lytic transglycosylase (by bulgecin) and penicillin-binding protein (by β-lactams) activities results in deformation of the septal cell wall, observed microscopically as a bulge preceding bacterial cell lysis. We describe a practical synthesis of the three naturally occurring bulgecin iminosaccharides and their mechanistic evaluation in a series of microbiological studies. These studies identify potentiation by the bulgecin at subminimum inhibitory concentrations of the β-lactam against three pathogenic Gram-negative bacteria and establish for the first time that this potentiation results in a significant increase in the bactericidal efficacy of a clinical β-lactam. 

Dik Data 2018


 Bacterial growth-curve assays and bacterial bulge-formation as visualized by microscopy. (a) Growth-curve assays of P. aeruginosa, E. aerogenes, and A. baumannii. The results for no antibiotic (yellow curve), 50 μg/mL bulgecin A (green curve), ceftazidime (CAZ; blue curve), and 50 μg/mL bulgecin A + CAZ (red curve) are shown. The sub-MIC concentrations of CAZ used for P. aeruginosa, E. aerogenes, and A. baumannii were 0.28, 8, and 2 μg/mL, respectively. (b) Confocal microscopy demonstrating that GFP-labeled P. aeruginosa grown in the presence of sub-MIC of CAZ exhibits elongation without bulges (on the left) and those grown in the presence of CAZ and bulgecin A exhibit elongation with bulges (on the right). The boxed area is expanded to highlight the bulges. A 10 μm scale bar is given in the top left corner. (c) In cell-wall homeostasis, lipid II is polymerized to the nascent peptidoglycan chain, comprised of repeats of the N-acetylglucosamine (NAG, light-green hexagons)−N-acetylmuramylpentapeptide (NAM, dark-green hexagons) disaccharide, by the transglycosylase (TG). The transpeptidase (TP) cross-links the nascent peptidoglycan to the growing edge of the cell wall. (d) β-Lactam antibiotics inhibit the TP activity, resulting in the accumulation of non-cross-linked nascent peptidoglycan, which serves as substrate for the lytic transglycosylase Slt in P. aeruginosa. Bulgecin A inhibits the Slt activity. Dual inhibition of Slt and TP results in the formation of the bulge, leading to the breached structural integrity of the cell wall.







“Four Core Facilities under One Umbrella”