Nonlinear elastodynamic behavior of intact and fractured rock under in-situ stress and saturation conditions
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Materials Science↗
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Microcomputed tomography (laboratory and synchrotron) of intact archeological human second metacarpa
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Stock, Stuart R.↗
Testing Os Staining Approach for Visualizing Soil Organic Matter Patterns in Intact Samples via X-ray Dual-Energy Tomography Scanning
Abstract not provided
Zheng, Hongbing↗
A spatiotemporally explicit and scalable indicator of intact lands across the conterminous United States, 1986–2023
Globally, ecologically intact areas are increasingly scarce. Agricultural expansion into previously uncultivated areas drives the loss of intact lands that might otherwise exhibit high levels of ecological integrity. Thus, the absence of cultivation can be an indicator of intact lands as measured from remote sensing data and thematic maps. Our objective for this study was to develop and compare tractable approaches based on remotely sensed satellite data to map spatial patterns of potentially intact lands across the conterminous U.S. (CONUS). Using annual cultivation probabilities derived from satellite observations, we classified and mapped potentially intact lands across CONUS from 1986 to 2023 at 30 m resolution. We created three maps, first by applying a constant cultivation probability threshold across CONUS, second by varying the threshold state-by-state to maximize state-level overall accuracies, and third by equalizing the state-level user's and producer's accuracies to minimize classification bias. Validation against 800,000+ independent ground samples resulted in CONUS-level overall accuracies ≥85% for the roughly 660 million ha of potentially intact land. Map accuracy varied with the proportion of potentially intact lands across regions, with the Pacific-Mountain and Great Plains regions exhibiting the highest accuracies, while Eastern CONUS exhibited a greater mix of potentially intact and non-intact lands and more moderate map accuracies. These novel maps and approaches can be adapted to different spatiotemporal extents to support conservation and production decisions ranging from species and ecosystems protection to reducing land conversion and climate mitigation.
agriculture↗
Experimental Investigation of Elastodynamic Nonlinear Response of Dry Intact, Fractured and Saturated Rock
Nonlinear elastodynamic response of fractured rocks carries crucial information on fracture features that can be exploited to forecast flow properties, friction constitutive behavior and poromechanical response. Well-controlled laboratory experiments are designed to measure the nonlinear elastodynamic response of Westerly granite in three states: dry intact, dry fractured and saturated fractured. We study the effect of fracturing and saturation in modifying the elastodynamic response of the rock. Each sample is tested at a normal stress level of 15 MPa. We measure the elastodynamic response of an intact L-shaped sample of Westerly Granite subjected to normal stress oscillations of prescribed amplitudes (0.2–1 MPa) and frequencies (0.1, 1, 10 Hz). Ultrasonic waves transmitted across the sample are used to monitor the evolution of wave velocity before, during and after dynamic stressing. Furthermore, the nonlinearity of the elastodynamic response is measured in terms of: (1) the offset in normalized wave velocity; (2) the amplitude of wave velocity fluctuation during the oscillations; and (3) recovery rate of the wave velocity post-oscillation. We observe that the three nonlinearity parameters show a similar trend. Irrespective of the parameter, the nonlinearity measures higher for sample in dry-intact condition than that for dry-fractured and the saturated-fractured sample exhibits smaller nonlinearity than the dry-fractured sample. As expected, the saturated sample exhibits less nonlinearity than the dry intact and fractured samples due to the presence of interstitial fluid and the resulting increased interface stiffness. Conversely, the dry intact rock shows a higher nonlinearity than the dry fractured. We use numerical simulations to show that the presence of fracture significantly alters the strain distribution across the bulk of the sample and only the contacting asperities are highly strained, thus resulting in a decrease in the measured elastodynamic nonlinearity.
58 GEOSCIENCES↗
Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy
In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t 1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4 + T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t 1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ~3 mo, the decay slope changes, and CD4 + T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.
2LTR circles↗
Best practices and benchmarks for intact protein analysis for top-down mass spectrometry
One gene can give rise to many functionally distinct proteoforms, each of which has a characteristic molecular mass. Many laboratories, however, forgo the challenging mass analysis of intact proteins. Instead, these researchers resort to well-established methods for proteolytic digests. In this work, the Consortium for Top-Down Proteomics (CTDP) addresses the unmet need for robust protocols for obtaining intact protein mass spectra. We quantify and rationalize the signal suppression associated with common interfering substances. A decision tree, based upon sample composition and experimental goals, guides researchers to a given protocol. Cross-platform analytical benchmarks are provided to allow users to gauge their proficiency and to promote method standardization. This work should permit users at any experience level to obtain high-quality intact mass spectra of native and denatured proteins from mixtures of varying complexity, including intact antibodies and membrane proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Intact mass spectrometry screening to optimize hydroxyl radical dose for protein footprinting
Hydroxyl radical protein footprinting (HRPF) using synchrotron radiation is a well-validated method to assess protein structure in the native solution state. In this method, X-ray radiolysis of water generates hydroxyl radicals that can react with solvent accessible side chains of proteins, with mass spectrometry used to detect the resulting labeled products. An ideal footprinting dose provides sufficient labeling to measure the structure but not so much as to influence the results. The optimization of hydroxyl radical dose is typically performed using an indirect Alexa488 fluorescence assay sensitive to hydroxyl radical concentration, but full evaluation of the experiment's outcome relies upon bottom-up liquid chromatography mass spectrometry (LC-MS) measurements to directly determine sites and extent of oxidative labeling at the peptide and protein level. A direct evaluation of the extent of labeling to provide direct and absolute measurements of dose and “safe” dose ranges in terms of, for example, average numbers of labels per protein, would provide immediate feedback on experimental outcomes prior to embarking on detailed LC-MS analyses. To this end, we describe an approach to integrate intact MS screening of labeled samples immediately following exposure, along with metrics to quantify the extent of observed labeling from the intact mass spectra. Intact MS results on the model protein lysozyme were evaluated in the context of Alexa488 assay results and a bottom-up LC-MS analysis of the same samples. In conclusion, this approach provides a basis for placing delivered hydroxyl radical dose metrics on firmer technical grounds for synchrotron X-ray footprinting of proteins, with explicit parameters to increase the likelihood of a productive experimental outcome. Further, the method directs approaches to provide absolute and direct dosimetry for all types of labeling for protein footprinting.
59 BASIC BIOLOGICAL SCIENCES↗
Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants
The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in macaques starting ART ~1 year after infection. Intact SIV genomes in circulating CD4+T cells showed triphasic decay with an initial phase slower than the decay of the plasma virus, a second phase faster than the second phase decay of intact HIV-1, and a stable third phase reached after 1.6–2.9 years. Hypermutated proviruses showed bi- or mono-phasic decay, reflecting different selective pressures. Viruses replicating at ART initiation had mutations conferring antibody escape. With time on ART, viruses with fewer mutations became more prominent, reflecting decay of variants replicating at ART initiation. Collectively, these findings confirm ART efficacy and indicate that cells enter the reservoir throughout untreated infection.
60 APPLIED LIFE SCIENCES↗
Forest structure and solar-induced fluorescence across intact and degraded forests in the Amazon
Tropical forest degradation (e.g., anthropogenic disturbances such as selective logging and fires) alters forest structure and function and influences the forest's carbon sink. In this study, we explored structure-function relationships across a variety of degradation levels in the southern Brazilian Amazon by 1) investigating how forest structural properties vary as a function of degradation history using airborne lidar data; 2) assessing the effects of degradation on solar-induced chlorophyll fluorescence (SIF) seasonality using TROPOMI data; and 3) quantifying the contribution of structural variables to SIF using multiple regression models with stepwise selection of lidar metrics. Forest degradation history was obtained through Landsat time-series classification. We found that fire, logging, and time since disturbance were major determinants of forest structure, and that forests affected by fires experienced larger variability in leaf area index (LAI), canopy height and vertical structure relative to logged and intact forests. Moreover, only recently burned forests showed significantly depressed SIF during the dry season compared to intact forests. Canopy height and the vertical distribution of foliage were the best predictors of SIF. Unexpectedly, we found that wet-season SIF was higher in active regenerating forests (~ 4 years after fires or logging) compared with intact forests, despite lower LAI. Furthermore, our findings help to elucidate the mechanisms of carbon accumulation in anthropogenically disturbed tropical forests and indicate that they can capture large amounts of carbon while recovering.
54 ENVIRONMENTAL SCIENCES↗
Illumination of Damage in Intact Rocks by Ultrasonic Transmission-Reflection and Digital Image Correlation
aboratory-scale experiments on intact rocks are critical to the development of physics-based fundamental understanding of various geophysical phenomena. In this work, the capability of ultrasonic wave transmission (T-mode) and reflection (R-mode) to monitor damage progression in uniaxially loaded prismatic intact rock specimens has been analyzed, as it is imperative to study the observations and document the capabilities of these techniques in a controlled environment. This study is novel in the sense that the R-mode linear ultrasonic testing (LUT) has been rarely employed in studying intact rock damage processes in a laboratory setting, with most of the studies utilizing a direct transmission (T-mode) approach or focusing on macroscopically fractured material. The two-dimensional digital image correlation (2-D DIC) full-field strain measurement approach was also used in-sync with the LUT monitoring to explicitly correlate the stress-induced damage in the specimens with the changes observed in the ultrasonic (T-mode and R-mode) signals. The results show that both the T-mode and R-mode LUT approaches are sensitive to detect the evolution of tensile and shear damage in the specimens, with the R-mode ultrasonic signals showing higher degree of sensitivity to the damage in the rocks, immediately following the initiation of damage in the rock volume.
58 GEOSCIENCES↗
Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir
The latent reservoir for HIV-1 in resting CD4 + T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4 + T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t 1/2 = 30.1 d) and a slower second phase (t 1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t 1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.
59 BASIC BIOLOGICAL SCIENCES↗
Influence of ion-pairing reagents on the separation of intact glycoproteins using hydrophilic-interaction liquid chromatography - high-resolution mass spectrometry
Hydrophilic-interaction liquid chromatography (HILIC) of intact proteins offers high-resolution separations of glycoforms of glycoproteins differing in the number of (neutral) glycans. However, to obtain efficient separations it is essential that the positively charged sites of the proteins are shielded by acidic (negative) ion-pair reagents (IPRs), so as to enhance the contribution of the hydroxyl groups of the (neutral) sugars in the glycoprotein. Here, we studied the influence of various IPRs that differ in physico-chemical properties, such as hydrophobicity and acidity, on the capillary-scale HILIC separation of intact (glyco)proteins. We evaluated the use of fluoroacetic acid (MFA), difluoroacetic acid (DFA), trifluoroacetic acid (TFA), and heptafluorobutyric acid (HFBA) as diluents for sample preparation, as solvents for sample loading on a reversed-phase trap prior to the HILIC separation, and as mobile-phase components for HILIC and HILIC-MS. To reduce the contribution of ion-exchange interaction with the (silica-based) stationary phase, we used an acrylamide-based monolithic column. We studied the influence of the different IPRs on each step of the separation of a mixture of proteins of different size and hydrophilicity and on the separation of the five glycoforms of ribonuclease B. The content of IPR in the sample was shown not to affect the separation and the MS detection. However, a low content of TFA and DFA in the mobile phase is favourable, as it reduces adduct formation and leads to higher signal intensity. The optimized HILIC conditions successfully resolved nine major glycoforms groups of a ~40 kDa glycoprotein horseradish peroxidase (HRP), as an example of a complex glycoprotein.
59 BASIC BIOLOGICAL SCIENCES↗
Intact archeological human bones and age at death studied with transmission x–ray diffraction and small angle x–ray scattering
In this work, high-energy, wide-angle x-ray scattering (WAXS, x-ray diffraction) and small-angle x-ray scattering (SAXS) were used to study intact human second metacarpal bones (mc2) from two UK archeological sites. A novel method correcting for irregular mass distribution was applied in these transmission geometry experiments done at beamline 1-ID of the Advanced Photon Source. The authors asked whether there were age-at-death-related changes in carbonated apatite (cAp) lattice parameters and whether SAXS could detect collagen D-period peaks in the archeological mc2. For each of the two sites, Ancaster and Wharram Percy in England, six female mc2s were studied; for each site, two were from each of three age-at-death cohorts (young, 18-29 years; middle, 30-49 years; old >= 50 years) along with a modern control mc2. The Rietveld method was applied to the WAXS patterns to provide precise lattice parameter values. The cAp lattice parameters did not correlate with age-at-death estimated from dental wear. From WAXS and the 00.2 diffraction peak widths, four archeological mc2s possessed coherently scattering domain lengths (crystallite c-axis sizes) that matched that of the modern mc2; SAXS revealed the same four archeological mc2 had D-period peak intensities equivalent to that of the modern mc2. The other eight archeological mc2s had significantly larger crystallite sizes (than the modern mc2) and weak or absent D-period peaks, differences attributed to diagenetic changes. Based on these data, the authors suggest that WAXS 00.2 peak width and SAXS D-period peak intensity can be used with intact bones to select those likely to retain largely unaltered tissue nanostructure, which might be required for other analyses. Taken as a whole, the results suggest detecting age-related deterioration in nanostructural features may be difficult in bone showing significant bioerosion.
59 BASIC BIOLOGICAL SCIENCES↗
Ion-Ion Proton Transfer and Parallel Ion Parking for the Analysis of Mixtures of Intact Proteins on a Modified Orbitrap Mass Analyzer
We have enabled parallel ion parking on a modified Orbitrap Elite™ as a way to control ion-ion proton transfer reactions via selective activation of a range of ions. The result is the concentration of the majority of ion current from multiple charge states of each precursor proteoform into a single charge state, maximizing signal intensity and increasing effective sensitivity compared to conventional MS1 spectra. These techniques were applied in an on-line HPLC, data-dependent MS/MS analysis of intact E. coli ribosomal proteins with HCD fragmentation. With one injection, all but two ribosomal proteins were selected for fragmentation and subsequently identified. The techniques described facilitate rapid identification of intact proteins in complex mixtures and an enhanced ability to observe proteins of low abundance. .
74 ATOMIC AND MOLECULAR PHYSICS↗
Splitting tensile strength of shale cores: intact versus fractured and sealed with ureolysis-induced calcium carbonate precipitation (UICP)
Ureolysis-induced calcium carbonate precipitation (UICP) is a biomineral solution where the urease enzyme converts urea and calcium into calcium carbonate. The resulting biomineral can bridge gaps in fractured shale, reduce undesired fluid flow, limit fracture propagation, better store carbon dioxide, and potentially enhance well efficiency. The mechanical properties of shale cores were investigated using a modified Brazilian indirect tensile strength test. An investigation of intact shale using Eagle Ford and Wolfcamp cores was conducted at varying temperatures. Results show no significant difference between shale types (average tensile strength = 6.19 MPa). Eagle Ford displayed higher strength at elevated temperature, but temperature did not influence Wolfcamp. Comparatively, cores with a single, lengthwise heterogeneous fracture were sealed with UICP and further tested for tensile strength. UICP was delivered via a flow-through method which injected 20–30 sequential patterns of ureolytic microorganisms and UICP-promoting fluids into the fracture until permeability reduced by three orders of magnitude or with an immersion method which placed cores treated with guar gum and UICP-promoting fluids into a batch reactor, demonstrating that guar gum is a suitable inclusion and may reduce the number of flow-through injections required. Tensile results for both delivery methods were variable (0.15–8 MPa), and in some cores the biomineralized fracture split apart, possibly due to insufficient sealing and/or heterogeneity in the composite UICP-shale cores. Notably in other cores the biomineralized fracture remained intact, demonstrating more cohesion than the surrounding shale, indicating that UICP may produce a strong seal for subsurface application.
58 GEOSCIENCES↗
Gold-Nanocluster-Mediated Delivery of siRNA to Intact Plant Cells for Efficient Gene Knockdown
RNA interference, which involves the delivery of small interfering RNA (siRNA), has been used to validate target genes, to understand and control cellular metabolic pathways, and to use as a "green" alternative to confer pest tolerance in crops. Conventional siRNA delivery methods such as viruses and Agrobacterium -mediated delivery exhibit plant species range limitations and uncontrolled DNA integration into the plant genome. Here, we synthesize polyethylenimine-functionalized gold nanoclusters (PEI-AuNCs) to mediate siRNA delivery into intact plants and show that these nanoclusters enable efficient gene knockdown. We further demonstrate that PEI-AuNCs protect siRNA from RNase degradation while the complex is small enough to bypass the plant cell wall. Consequently, AuNCs enable gene knockdown with efficiencies of up 76.5 ± 5.9% and 76.1 ± 9.5% for GFP and ROQ1, respectively, with no observable toxicity. Our data suggest that AuNCs can deliver siRNA into intact plant cells for broad applications in plant biotechnology.
59 BASIC BIOLOGICAL SCIENCES↗
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria
Chemical cues mediate interactions between marine phytoplankton and bacteria, underpinning ecosystem-scale processes including nutrient cycling and carbon fixation. Phage infection alters host metabolism, stimulating the release of chemical cues from intact plankton, but how these dynamics impact ecology and biogeochemistry is poorly understood. Here we determine the impact of phage infection on dissolved metabolite pools from marine cyanobacteria and the subsequent chemotactic response of heterotrophic bacteria using time-resolved metabolomics and microfluidics. Metabolites released from intact, phage-infected Synechococcus elicited strong chemoattraction from Vibrio alginolyticus and Pseudoalteromonas haloplanktis, especially during early infection stages. Sustained bacterial chemotaxis occurred towards live-infected Synechococcus, contrasted by no discernible chemotaxis towards uninfected cyanobacteria. High-throughput microfluidics identified 5′-deoxyadenosine and 5′-methylthioadenosine as key attractants. Our findings establish that, before lysis, phage-infected picophytoplankton release compounds that attract motile heterotrophic bacteria, suggesting a mechanism for resource transfer that might impact carbon and nutrient fluxes across trophic levels.
Henshaw, Richard J↗