Publications at our Core: Core Impact

Core facility scientists are partners in the advancement of knowledge.  Whether advancing capabilities of instrumentation or collecting critical data for a figure (or cover), core staff collaborations with faculty and students drive research at NU! In 2017 core facility staff were co-authors on over 85 peer reviewed publications and core facilities provided key data for over 1,000 publications. See recent examples of core contributions below.
*For information on when anyone providing assistance with generation of data for a publication should be considered for an acknowledgment or authorship, consult the Core Facilities Administration's Publication Guidelines for Users of Core Facilities.

The lateral resolution of scanning thermal microscopy (SThM) has hitherto never approached that of mainstream atomic force microscopy, mainly due to poor performance of the thermal sensor. We have developed a thermocouple-based probe technology delivers excellent lateral resolution (∼20 nm), extended high-temperature measurements >700 °C without cantilever bending, and thermal sensitivity (∼0.04 °C). The origin of significantly improved figures-of-merit lies in the probe design that consists of a hollow silicon tip integrated with a vertically oriented thermocouple sensor at the apex (low thermal mass) which interacts with the sample through a metallic nanowire (50 nm diameter), thereby achieving high lateral resolution. The nanoscale pitch and extremely small thermal mass of the probe promise significant improvements over existing methods and wide range of applications in several fields including semiconductor industry, biomedical imaging, and data storage.

 

 

The Center for Advanced Microscopy: Reflectance imaging for visualization of unlabeled structures using Nikon A1 and N-SIM; Dr. Emily J Guggenheim, and Dr. Joshua Z Rappoport; https://www.nikoninstruments.com/Learn-Explore/Application-Notes/N-SIM-and-N-SIM-E/Reflectance-imaging-for-visualization-of-unlabeled-structures-using-Nikon-A1-and-N-SIM
The Center for Advanced Microscopy is home to the Nikon Imaging Center and core staff collaborate extensively with Nikon to evaluate new instrumentation and develop state-of-the-art techniques to image real world samples.  In the application note, the Nikon A1 and N-SIM instruments were optimized to image nanoparticle incorporation into live cells and demonstrated semi-quantitative analysis of ceria, iron oxide, gold, and silver nanoparticles.  These types of particles are opaque and therefore not amenable to transmission based techniques.  The instruments had to be modified to eliminate scattering artifacts due to the cellular components in order to acheive sufficient signal to noise needed to identify the individual nanoparticles. When combined with staining techniques, the location of nanoparticles can be easily determined. Characterization of the concentration and intracellular location of metal oxide nanoparticles is critical to understanding the possible environmental impacts of the use of these materials which rapidly penetrate cellular membranes.

 

Data collected in the Integrated Molecular Structure Education and Research Center (IMSERC) was featured on the cover ofChemistry of Materials describing best practices for metal-organic framework materials (MOF’s). MOF’s have record breaking surface areas and applications in gas storage and catalysis applications. IMSERC single crystal X-Ray diffraction, powder X-Ray diffraction, mass spectrometry and NMR spectrometry were used to characterize bulk materials and novel organic linkers. The ability to collect single crystal XRD data on crystals with <100mm/side has rapidly increased the rate of development in this field.

 

 

 

 

 

The development of massively parallel genome sequencing technologies has led to a paradigm shift in biomedical research, and the emergence of precision medicine. Scientists and clinicians are now able to see how human diseases and phenotypic changes are connected to DNA sequence changes, genome structural changes, and epigenomic abnormality. Next-Generation Sequencing Data Analysis, authored by the director of the Northwestern University NUSeq Core Facility, provides a practical guide to applying these powerful genome technologies to major areas of biomedical research. 

The book walks readers through multiple stages of NGS data generation and analysis in an easy-to-follow fashion. It covers every step in each stage, from the planning stage of experimental design, sample processing, sequencing strategy formulation, the early stage of base calling, reads quality check and data preprocessing to the intermediate stage of mapping reads to a reference genome and normalization to more advanced stages specific to each application. All major applications of NGS are covered, including: RNA-seq: gene expression analysis, Genome re-sequencing: genotyping and variant discovery, De novo genome assembly, ChIP-seq: study of DNA–protein interaction, DNA methyl-seq: epigenomic regulation, Microbiome sequencing.