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1. A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer

   Martin R. O’Steen, Dmitry M. (November 2022, Sensors and Actuators Reports)

   Multiplex assays often rely on expensive sensors incorporating covalently linked fluorescent dyes. Herein, we developed a self-assembling aptamer-based multiplex assay. This multiplex approach utilizes a previously established split aptamer sensor in conjugation with a novel split aptamer sensor based upon a malachite green DNA aptamer. This system was capable of simultaneous fluorescent detection of two SARS COVID-19-related sequences in one sample with individual sensors that possesses a limit of detection (LOD) in the low nM range. Optimization of the Split Malachite Green (SMG) sensor yielded a minimized aptamer construct, Mini-MG, capable of inducing fluorescence of malachite green in both a DNA hairpin and sensor format. 

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2. Topography and canopy cover influence soil organic carbon composition and distribution across a forested hillslope in the discontinuous permafrost zone

   https://doi.org/10.1002/ppp.2200  

   Rooney, Erin C.; Bailey, Vanessa L.; Patel, Kaizad F.; Kholodov, Alexander; Golightly, Holly; Lybrand, Rebecca A. (July 2023, Permafrost and Periglacial Processes)

   Abstract Topography and canopy cover influence ground temperature in warming permafrost landscapes, yet soil temperature heterogeneity introduced by mesotopographic slope positions, microtopographic differences in vegetation cover, and the subsequent impact of contrasting temperature conditions on soil organic carbon (SOC) dynamics are understudied. Buffering of permafrost‐affected soils against warming air temperatures in boreal forests can reflect surface soil characteristics (e.g., thickness of organic material) as well as the degree and type of canopy cover (e.g., open cover vs. closed cover). Both landscape and soil properties interact to determine meso‐ and microscale heterogeneity of ground warming. We sampled a hillslope catena transect in a discontinuous permafrost zone near Fairbanks, Alaska, to test the small‐scale (1 to 3 m) impacts of slope position and cover type on soil organic matter composition. Mineral active layer samples were collected from backslope, low backslope, and footslope positions at depths spanning 19 to 60 cm. We examined soil mineralogical composition, soil moisture, total carbon and nitrogen content, and organic mat thickness in conjunction with an assessment of SOC composition using Fourier‐transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS). Soils in the footslope position had a higher relative contribution of lignin‐like compounds, whereas backslope soils had more aliphatic and condensed aromatic compounds as determined using FT‐ICR‐MS. The effect of open versus closed tree canopy cover varied with the slope position. On the backslope, we found higher oxidation of molecules under open cover than closed cover, indicating an effect of warmer soil temperature on decomposition. Little to no effect of the canopy was observed in soils at the footslope position, which we attributed, in part, to the strong impact of soil moisture content in SOC dynamics in the water‐gathering footslope position. The thin organic mat under open cover on the backslope position may have contributed to differences in soil temperature and thus SOC oxidation under open and closed canopies. Here, the thinner organic mat did not appear to buffer the underlying soil against warm season air temperatures and thus increased SOC decomposition as indicated by the higher oxidation of SOC molecules and a lower contribution of simple molecules under open cover than the closed canopy sites. Our findings suggest that the role of canopy cover in SOC dynamics varies as a function of landscape position and soil properties, namely, organic mat thickness and soil moisture. Condition‐specific heterogeneity of SOC composition under open and closed canopy cover highlights the protective effect of canopy cover for soils on backslope positions. 

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3. Structural and kinetic basis for the regulation and potentiation of Hsp104 function

   https://doi.org/doi.org/10.1073/pnas.192196811  

   Xiang Ye https:/ and S. Walter Englander (April 2020, PNAS nexus)

   Hsp104 provides a valuable model for the many essential proteostatic functions performed by the AAA+ superfamily of protein molecular machines. We developed and used a powerful hydrogen exchange mass spectrometry (HX MS) analysis that can provide positionally resolved information on structure, dynamics, and energetics of the Hsp104 molecular machinery, even during functional cycling. HX MS reveals that the ATPase cycle is rate-limited by ADP release from nucleotide-binding domain 1 (NBD1). The middle domain (MD) serves to regulate Hsp104 activity by slowing ADP release. Mutational potentiation accelerates ADP release, thereby increasing ATPase activity. It reduces time in the open state, thereby decreasing substrate protein loss. During active cycling, Hsp104 transits repeatedly between whole hexamer closed and open states. Under diverse conditions, the shift of open/closed balance can lead to premature substrate loss, normal processing, or the generation of a strong pulling force. HX MS exposes the mechanisms of these functions at near-residue resolution. 

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4. Structural and kinetic basis for the regulation and potentiation of Hsp104 function

   https://doi.org/10.1073/pnas.1921968117  

   Ye, Xiang; Lin, JiaBei; Mayne, Leland; Shorter, James; Englander, S. Walter (April 2020, Proceedings of the National Academy of Sciences)

   Hsp104 provides a valuable model for the many essential proteostatic functions performed by the AAA+ superfamily of protein molecular machines. We developed and used a powerful hydrogen exchange mass spectrometry (HX MS) analysis that can provide positionally resolved information on structure, dynamics, and energetics of the Hsp104 molecular machinery, even during functional cycling. HX MS reveals that the ATPase cycle is rate-limited by ADP release from nucleotide-binding domain 1 (NBD1). The middle domain (MD) serves to regulate Hsp104 activity by slowing ADP release. Mutational potentiation accelerates ADP release, thereby increasing ATPase activity. It reduces time in the open state, thereby decreasing substrate protein loss. During active cycling, Hsp104 transits repeatedly between whole hexamer closed and open states. Under diverse conditions, the shift of open/closed balance can lead to premature substrate loss, normal processing, or the generation of a strong pulling force. HX MS exposes the mechanisms of these functions at near-residue resolution. 

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5. Examining the mass loss and thermal properties of 3D printed models produced by fused deposition modeling and stereolithography under elevated temperatures

   https://doi.org/10.1108/RPJ-01-2022-0007  

   Hsieh, Shu-An; Anderson, Jared L. (June 2022, Rapid Prototyping Journal)

   Purpose This paper aims to study the mass loss of three-dimensional (3D) printed materials at high temperatures. A preconcentration and analysis technique, static headspace gas chromatography-mass spectrometry (SHS-GC-MS), is demonstrated for the analysis of volatile compounds liberated from fused deposition modeling (FDM) and stereolithography (SLA) 3D printed models under elevated temperatures. Design/methodology/approach A total of seven commercial 3D printing materials were tested using the SHS-GC-MS approach. The printed model mass and mass loss were examined as a function of FDM printing parameters including printcore temperature, model size and printing speed, and the use of SLA postprocessing procedures. A high temperature resin was used to demonstrate that thermal degradation products can be identified when the model is incubated under high temperatures. Findings At higher printing temperatures and larger model sizes, the initial printed model mass increased and showed more significant mass loss after thermal incubation for FDM models. For models produced by SLA, the implementation of a postprocessing procedure reduced the mass loss at elevated temperatures. All FDM models showed severe structural deformation when exposed to high temperatures, while SLA models remained structurally intact. Mass spectra and chromatographic retention times acquired from the high temperature resin facilitated identification of eight compounds (monomers, crosslinkers and several photoinitiators) liberated from the resin. Originality/value The study exploits the high sensitivity of SHS-GC-MS to identify thermal degradation products emitted from 3D printed models under elevated temperatures. The results will aid in choosing appropriate filament/resin materials and printing mechanisms for applications that require elevated temperatures. 

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