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Physical distancing and inaccessibility to laboratory facilities created an opportunity to transition undergraduate research experiences to remote, digital platforms, adding another level of pedagogy to their training. Basic bioinformatics skills together with critical analysis of scientific literature are essential for addressing research questions in modern biology. The work presented here describes a fully online, collaborative research experience created to allow undergraduate students to learn those skills. The research experience was focused on the development and implementation of the Organonitrogen Biodegradation Database (ONDB, z.umn.edu/ondb). The ONDB was developed to catalog information about the cost, chemical properties, and biodegradation potential of commonly used organonitrogen compounds. A cross-institutional team of undergraduate researchers worked in collaboration with two faculty members and a postdoctoral fellow to develop the database. Students carried out extensive online literature searches and used a biodegradation prediction website to research and represent the microbial catabolism of different organonitrogen compounds. Participants employed computational tools such as R, Shiny, and flexdashboard to construct the database pages and interactive web interface for the ONDB. Worksheets and forms were created to encourage other students and researchers to gather information about organonitrogen compounds and expand the database. Student progress was evaluated through biweekly project meetings, presentations, and a final reflection. The ONDB undergraduate research experience provided a platform for students to learn bioinformatics skills while simultaneously developing a teaching and research tool for others., (©2021 Author(s). Published by the American Society for Microbiology.)

X-ray imaging using a Talbot-Lau interferometer, consisting of three binary gratings, is a well-established approach to acquire x-ray phase-contrast and dark-field images with a polychromatic source. However, challenges in the production of high aspect ratio gratings limit the construction of a compact setup for high x-ray energies. In this study we consider the use of phase gratings with triangular-shaped structures in an x-ray interferometer and show that such gratings can yield high visibilities for significantly shorter propagation distances than conventional gratings with binary structures. The findings are supported by simulation and experimental results for both cases of a monochromatic and a polychromatic source.

X-ray dark-field scatter imaging allows to gain information on the average local direction and anisotropy of micro-structural features in a sample well below the actual detector resolution. For thin samples the morphological interpretation of the signal is straight forward, provided that only one average orientation of sub-pixel features is present in the specimen. For thick samples, however, where the x-ray beam may pass structures of many different orientations and dimensions, this simple assumption in general does not hold and a quantitative description of the resulting directional dark-field signal is required to draw deductions on the morphology. Here we present a description of the signal formation for thick samples with many overlying structures and show its validity in experiment. In contrast to existing experimental work this description follows from theoretical predictions of a numerical study using a Fourier optics approach. One can easily extend this description and perform a quantitative structural analysis of clinical or materials science samples with directional dark-field imaging or even direction-dependent dark-field CT.

The understanding of large biophysical systems at the systems level often depends on a precise knowledge of their microstructure. This is difficult to obtain, especially in vivo, because most imaging methods are either limited in terms of achievable field of view, or make use of penetrating ionizing radiations such as x-rays, in which case the resolution is severely limited by the deposited dose. Here, we describe a new method, x-ray vector radiography (XVR), which yields various types of information about the local orientation, anisotropy and average size of the sample microstructures. We demonstrate the feasibility by showing first experimental XVRs of human vertebra bone samples, giving information on the trabecular structures even with a pixel resolution of half a millimetre, much larger than the structures themselves. This last point is critical for the development of low-dose measurement methods which will allow for in vivo studies and potentially in the future for new medical diagnostics methods of bone metabolic disorder diseases such as osteoporosis.