Search

Start Over Domain Natural Sciences Type Dataset Year Published 2020

1. A dual-mechanism antibiotic kills Gram-negative bacteria and avoids drug resistance

Author(s):
Martin, James K; Sheehan, Joseph P; Bratton, Benjamin P; Moore, Gabriel M; Mateus, André; Li, Sophia Hsin-Jung; Kim, Hahn; Rabinowitz, Joshua D; Typas, Athanasios; Savitski, Mikhail M; Wilson, Maxwell Z; Gitai, Zemer
Abstract:
The rise of antibiotic resistance and declining discovery of new antibiotics have created a global health crisis. Of particular concern, no new antibiotic classes have been approved for treating Gram-negative pathogens in decades. Here, we characterize a compound, SCH-79797, that kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism of action (MoA) with undetectably-low resistance frequencies. To characterize its MoA, we combined quantitative imaging, proteomic, genetic, metabolomic, and cell-based assays. This pipeline demonstrates that SCH-79797 has two independent cellular targets, folate metabolism and bacterial membrane integrity, and outperforms combination treatments in killing MRSA persisters. Building on the molecular core of SCH-79797, we developed a derivative, Irresistin-16, with increased potency and showed its efficacy against Neisseria gonorrheae in a mouse vaginal infection model. This promising antibiotic lead suggests that combining multiple MoAs onto a single chemical scaffold may be an underappreciated approach to targeting challenging bacterial pathogens.
Type:
Dataset
Issue Date:
20 May 2020

4. Data from a flume experiment of passive scalar diffusion within vegetation canopies using laser-induced fluorescence

Author(s):
Ghannam, Khaled; Poggi, Davide; Katul, Gabriel; Bou-Zeid, Elie
Abstract:
This dataset is a sequence of laser-induced fluorescence images of a dye injected in a channel flow with canopy-like stainless steel rods simulating a vegetation canopy stand. The data is acquired close to the channel bottom at z/h=0.2, where z is the height referenced to the channel bed and h is the canopy height. The dataset provides spatial distribution of scalar concentration in a plane parallel to the channel bed. The data has been used (but the data itself has not been published or available to the public) in previous work. The references are: Ghannam, K., Poggi, D., Porporato, A., & Katul, G. (2015). The spatio-temporal statistical structure and ergodic behaviour of scalar turbulence within a rod canopy. Boundary-Layer Meteorology,157(3), 447–460. Ghannam, K, Poggi, D., Bou-Zeid, E., Katul, G. (2020). Inverse cascade evidenced by information entropy of passive scalars in submerged canopy flows. Geophysical Research Letters (accepted).
Type:
Dataset
Issue Date:
22 April 2020

5. Dataset for 'Auditory Activity is Diverse and Widespread Throughout the Central Brain of Drosophila'

Author(s):
Pacheco, Diego A; Thiberge, Stephan; Pnevmatikakis, Eftychios; Murthy, Mala
Abstract:
Sensory pathways are typically studied starting at receptor neurons and following postsynaptic neurons into the brain. However, this leads to a bias in analysis of activity towards the earliest layers of processing. Here, we present new methods for volumetric neural imaging with precise across-brain registration, to characterize auditory activity throughout the entire central brain of Drosophila and make comparisons across trials, individuals, and sexes. We discover that auditory activity is present in most central brain regions and in neurons responsive to other modalities. Auditory responses are temporally diverse, but the majority of activity is tuned to courtship song features. Auditory responses are stereotyped across trials and animals in early mechanosensory regions, becoming more variable at higher layers of the putative pathway, and this variability is largely independent of spontaneous movements. This study highlights the power of using an unbiased, brain-wide approach for mapping the functional organization of sensory activity.
Type:
Dataset
Issue Date:
October 2020

6. Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori

Author(s):
Taylor, Jenny A.; Bratton, Benjamin P.; Sichel, Sophie R.; Blair, Kris M.; Jacobs, Holly M.; DeMeester, Kristen E.; Kuru, Erkin; Gray, Joe; Biboy, Jacob; VanNieuwenhze, Michael S.; Vollmer, Waldemar; Grimes, Catherine L.; Shaevitz, Joshua W.; Salama, Nina R.
Abstract:
Helical cell shape is necessary for efficient stomach colonization by Helicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-type H. pylori cells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with either N-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.
Type:
Dataset and Image
Issue Date:
April 2019

8. Femtosecond X-ray Diffraction of Laser-shocked Forsterite (Mg2SiO4) to 122 GPa

Author(s):
Kim, Donghoon; Tracy, Sally J.; Smith, Raymond F.; Gleason, Arianna E.; Bolme, Cindy A.; Prakapenka, Vitali B.; Appel, Karen; Speziable, Sergio; Wicks, June K.; Berryman, Eleanor J.; Han, Sirus K.; Schoelmerich, Markus O.; Lee, Hae Ja; Nagler, Bob; Cunningham, Eric F.; Akin, Minta C.; Asimow, Paul D.; Eggert, Jon H.; Duffy, Thomas S.
Abstract:
The behavior of forsterite, Mg2SiO4, under dynamic compression is of fundamental importance for understanding its phase transformations and high-pressure behavior. Here, we have carried out an in situ X-ray diffraction study of laser-shocked poly- and single-crystal forsterite (a-, b-, and c- orientations) from 19 to 122 GPa using the Matter in Extreme Conditions end-station of the Linac Coherent Light Source. Under laser-based shock loading, forsterite does not transform to the high-pressure equilibrium assemblage of MgSiO3 bridgmanite and MgO periclase, as was suggested previously. Instead, we observe forsterite and forsterite III, a metastable polymorph of Mg2SiO4, coexisting in a mixed-phase region from 33 to 75 GPa for both polycrystalline and single-crystal samples. Densities inferred from X-ray diffraction data are consistent with earlier gas-gun shock data. At higher stress, the behavior observed is sample-dependent. Polycrystalline samples undergo amorphization above 79 GPa. For [010]- and [001]-oriented crystals, a mixture of crystalline and amorphous material is observed to 108 GPa, whereas the [100]-oriented crystal adopts an unknown crystal structure at 122 GPa. The Q values of the first two sharp diffraction peaks of amorphous Mg2SiO4 show a similar trend with compression as those observed for MgSiO3 glass in both recent static and laser-compression experiments. Upon release to ambient pressure, all samples retain or revert to forsterite with evidence for amorphous material also present in some cases. This study demonstrates the utility of femtosecond free-electron laser X-ray sources for probing the time evolution of high-pressure silicates through the nanosecond-scale events of shock compression and release.
Type:
Dataset
Issue Date:
November 2020

9. First impurity powder injection experiments in LHD

Author(s):
Nespoli, F; Ashikawa, N.; Gilson, E. P.; Lunsford, R.; Masuzaki, S.; Shoji, M.; Oishi, T.; Suzuki, C.; Nagy, A.; Mollén, A.; Pablant, N. A.; Ida, K.; Yoshinuma, M.; Tamura, N.; Gates, D. A.; Morisaki, T.; experiment group, LHD
Type:
Dataset
Issue Date:
2020