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Transcriptome responses to single and combined stressors in seagrass populations from pristine and impacted sites reveal local adaptive features and core stress-response genes
No full textIn their natural habitats, seagrasses face multiple abiotic stressors, which can often occur simultaneously. However, most studies have only focused on growth and physiological responses to single stressors. Here, we examined transcriptome responses of the tropical seagrass Halophila stipulacea collected from a northern Gulf of Aqaba pristine site and an anthropogenically-impacted site, grown in a mesocosm, and exposed to ecologically-relevant, single and combined, thermal and excess nutrient stressors. Growth of plants from the impacted site was more tolerant to stress than plants from the pristine site. The combined thermal and nutrient stressor elicited greater transcriptome reprogramming than the single stressors in both populations and induced the expression of a combination-specific set of genes involved in stress responses. Furthermore, thermal stress exerted a dominant influence upon the transcriptome response to the combined stressor. Transcriptomes of plants from the impacted site displayed reduced responsiveness to stress, the presence of genes exhibiting a “stress-ready” mode of expression under all stressors, and increased resilience (recovery to control transcriptomes). We also identified core stress-response genes that could be leveraged as early indicators of stress in the field. Overall, our data suggest that environmental conditions in seagrass habitats can drive local molecular adaptation, and that the response of seagrasses to combined stressors associated with climate change and coastal anthropogenic stressors cannot be predicted from the response to single stressors
Mössbauer studies of the redox state of the ferric uptake regulator [2Fe–2S]2+ cluster in Escherichia coli
No full textThe Ferric uptake regulator (Fur) proteins from Haemophilus influenzae and Escherichia coli overexpressed in E. coli cells (MC4100) grown in M9 medium supplemented with 57Fe were studied with Mössbauer spectroscopy. Previous studies have shown that Fur proteins from H. influenzae and E. coli bind a [2Fe–2S]2+ cluster in response to elevation of intracellular free iron content. Here we find that when the [2Fe–2S]2+ clusters in purified Fur proteins are reduced with dithionite, the reduced clusters are quickly decomposed, forming compounds with two distinct spectral signatures of high spin Fe(II) in tetrahedral and octahedral coordination, respectively. The instability of the reduced [2Fe-2S]1+ cluster in Fur is unique, as the [2Fe–2S]2+ clusters in many other proteins can reversibly undergo one-electron reduction-oxidation. The Mössbauer spectra of whole E. coli cells overexpressing Fur proteins show a quadrupole doublet with the isomer shift of δ1 = 0.28 mm/s and ΔEQ1 = 0.52 mm/s, typical for oxidized [2Fe-2S]2+ clusters and identical with that in the purified Fur protein. The corresponding spectra in large applied magnetic fields show the diamagnetic pattern that unambiguously reveals an exchange-coupled system with a diamagnetic electronic ground state, which confirms its assignment to the oxidized [2Fe-2S]2+ cluster clusters from Fur. No reduced [2Fe-2S]1+ clusters of Fur are observed in the whole-cell E. coli spectra. The Mössbauer spectra of the whole-cell E. coli without the Fur expression do not contain the components associated with the [2Fe–2S]2+ cluster of Fur
Three distinct forms of Pneumocystis coexist in individuals of two species of deer mice (genus Peromyscus)
No full textAs emerging zoonoses represent a significant public health threat, understanding how pathogens\u27 host ranges evolve is critical to protect human and wildlife health. Closely related hosts infected with host-specific pathogens provide valuable opportunities for clear inferences of host range evolution, as they allow for the examination of early diversification patterns in their resident pathogens. Pneumocystis, an obligate lung symbiont that is believed to be ubiquitous in mammals, exemplifies such a model. To explore the early stages of divergence in Pneumocystis, we collected geographically dispersed samples from two sister species of deer mice: Peromyscus leucopus (white-footed mice) and Peromyscus gossypinus (cotton mice). We sequenced two nuclear and two mitochondrial loci of Pneumocystis sampled from the lungs of these mice. These sequences revealed three distinct Pneumocystis taxa, two of which were found to cross-infect both host species and were often found coexisting within the same individual. Genetic diversity and phylogenetic analysis suggest that the three Pneumocystis taxa represent separate species. Further analysis of the mitochondrial large subunit rRNA gene from the most common taxon of these three revealed that host geographic origins influenced Pneumocystis genetic structure more than host species identity. Nevertheless, the results also suggest an overall interconnectedness of the symbiont metapopulation
Computational Search for Multimetallic Alloys to Replace Precious Metal Catalysts for Formate Dehydrogenation
No full textPrecious noble metal catalysts are widely used in the chemical industry because of their unique surface reactivity and selectivity. For certain reactions, however, the high cost of these catalysts can hinder their economic feasibility. For instance, formate-salt dehydrogenation offers a promising, reversible, on‑demand H₂ storage and transport method under mild conditions. This approach can potentially link large‑scale H₂ production with end‑use applications. The most active catalysts for formate salt dehydrogenation are Pd and Pd‑based alloys such as AuPd and AgPd nanoparticles. Yet these materials remain expensive, prone to deactivation, and still fall short in activity. Unless a less costly, more active catalyst can be designed, formate salts will struggle to achieve commercial viability as hydrogen carriers.
To address this, we have performed a theoretical search for multimetallic disordered alloys that can mimic the catalytic performance of AuPd. To begin with, we hypothesize that the surface reactivity of the catalyst is controlled primarily by the bulk electronic structure. Therefore, we combined a Genetic Algorithm (GA) with electronic structure calculations based on the Korringa–Kohn–Rostoker Coherent Potential Approximation (KKR‑CPA) to identify compositionally random alloys whose density of states replicates that of AuPd. As a result, three ternary candidates were identified: Ag0.40Ni0.20Pd0.40, Ag0.40Cu0.30Ni0.30, and Ag0.40Cu0.20Pd0.40. Since no finite supercell can uniquely represent a disordered alloy phase, we leveraged the Virtual Crystal Approximation (VCA) approach to perform calculations to investigate the surface reactivity of these alloys. The adsorption energy of atomic hydrogen is chosen to illustrate this approach, both for its simplicity and for the strong relevance of H in renewable energy applications including formate dehydrogenation. H adsorption energies are computed on adsorption sites with all possible compositions of its first coordination shell (i.e. the nearest-neighbor atoms directly surrounding the site) on the close-packed facet of each ternary alloy. Then, Gaussian distributions were applied to approximate the distributions of adsorption energies as a result of completely random atomic arrangements in the surface. The results suggest that the selected alloys hold promise for replicating the surface reactivity of AuPd. Pending future experimental validation, this approach could prove effective in guiding the design of cost‑effective, high‑performance catalysts for a variety of applications, reducing reliance on scarce noble metals
2024 VCP International Conference: Exploring multi-disciplinary approaches from basic science of valosin containing protein, an AAA+ ATPase protein, to the therapeutic advancement for VCP-associated multisystem proteinopathy
No full textValosin-containing protein (VCP/p97) is a ubiquitously expressed AAA+ ATPase associated with numerous protein-protein interactions and critical cellular functions including protein degradation and clearance, mitochondrial homeostasis, DNA repair and replication, cell cycle regulation, endoplasmic reticulum-associated degradation, and lysosomal functions including autophagy and apoptosis. Autosomal-dominant missense mutations in the VCP gene may result in VCP-associated multisystem proteinopathy (VCP-MSP), a rare degenerative disorder linked to heterogeneous phenotypes including inclusion body myopathy (IBM) with Paget\u27s disease of bone (PDB) and frontotemporal dementia (FTD) or IBMPFD, amyotrophic lateral sclerosis (ALS), Alzheimer\u27s disease (AD), parkinsonism, Charcot-Marie Tooth disease (CMT), and spastic paraplegia. The complexity of VCP-MSP makes collaboration among stakeholders essential and necessitates a multi-disciplinary approach. The 2024 VCP International Conference was hosted at Caltech between February 22 and 25. Co-organized by Cure VCP Disease and Dr. Tsui-Fen Chou, the meeting aimed to center the patient as a research partner, harmonize diverse stakeholder engagement, and bridge the gap between basic and clinical neuroscience as it relates to VCP-MSP. Over 100 multi-disciplinary experts attended, ranging from basic scientists to clinicians to patient advocates. Attendees discussed genetics and clinical presentation, cellular and molecular mechanisms underlying disease, therapeutic approaches, and strategies for future VCP research. The conference included three roundtable discussions, 29 scientific presentations, 32 scientific posters, nine patient and caregiver posters, and a closing discussion forum. The following conference proceedings summarize these sessions, highlighting both the identified gaps in knowledge and the significant strides made towards understanding and treating VCP diseases
Unraveling the Heterogeneous but Ordered Microstructure of the Nonionic Deep Eutectic Solvent Formed by Lauric Acid and N-Methylacetamide
No full textThe nonionic deep eutectic solvent, formed by lauric acid (LA) and N-methylacetamide (NMA), has been shown to have a heterogeneous molecular structure in which the LA and NMA form nonpolar and polar domains, respectively. Previous vibrational spectroscopy experiments demonstrated that the ability of the LA domains to solvate compounds was limited to long carbon chains, whereas other nonpolar molecules, such as W(CO)6, were found to be solvated by both LA and NMA. These experiments were not fully compatible with the previously proposed micelle-like structure of the nonpolar domains of the LA-NMA DES. In this work, the modeling of the DES molecular structure is pursued using classical molecular dynamics simulations. The new classical model reproduces both the SAXS structural factors and the previously experimentally derived interaction map for these LA-NMA DESs. In addition, the simulation also shows that LA-NMA DESs form highly organized LA aggregates that are difficult to disorganize. Further evidence of the correct description provided by the newly derived model is obtained using a moderately polar probe: chloroform-d. Computations using the classical model have a good agreement with the solvation behavior of the probe derived from experiments, in which the location of the probe is found to be mostly within the polar domain of the DES. The computational model also demonstrates that the probe solvation is a consequence of the tightly packed LA structure, which causes nonpolar molecules to be located at the interphase of the DES nonpolar domains
Sulfur in Martian magmas from sulfur concentration at sulfide saturation applied to regional chemical maps
Get PDFThe sulfur cycle on Mars plays a critical role in shaping its surface and atmospheric chemistry. Mars\u27 near-surface sulfur inventory largely originated from mantle-derived magmas that erupted during the Noachian, Hesperian, and Amazonian eons. Satellites permit measurements of bulk sulfur in Martian regolith, and rover and meteorite measurements capture snapshots of sulfur in specific samples. However, the concentration of sulfur in Martian magmas prior to degassing, which governs the transfer of interior sulfur to the near-surface, remains uncertain. Because Mars\u27 mantle may be sulfur-rich, most primary mantle melts are expected to be in equilibrium with residual mantle sulfide. In this work, we therefore use Gamma Ray Spectroscopy (GRS) regional maps of bulk surface chemistry to calculate the sulfur concentration at sulfide saturation (SCSS) for late Noachian through Amazonian Martian magmas. We further consider a range in mantle source sulfur and constraints on degree of melting to account for mantle sulfide exhaustion, in order to estimate sulfur concentrations in primitive melts. We find that the concentration of sulfur in Martian magmas ranged between ∼1330 and 4550 ppm S. These results underscore that the GRS sulfur concentration data, from ∼15,000 and 29,000 ppm globally, do not represent the sulfur content of primitive basalts, but rather reflect myriad processes that cycled sulfur within the critical zone of exchange between the atmosphere and crust. We define a new metric, the Sulfur Enrichment Index (SEI), that tracks the enrichment in present-day regolith sulfur relative to the original magmatic sulfur concentration in volcanic regions. We show that sulfur release is inefficient for magmas emplaced at \u3e1–2 km depth. Accounting for the total extruded volume of magma from the late Noachian through the Amazonian, our estimates of primary magmatic sulfur concentrations lead to a cumulative yield of ∼2–68 × 1019 g of sulfur to the Martian atmosphere from ∼3.8 Ga to the present. For comparison, only ∼1018–1019 g of sulfur is now hosted within the upper decimeters of the Martian crust at mid-latitudes. We therefore infer that volcanogenic sulfur, like water, has likely been sequestered within Mars\u27 crust
HIGH-PERFORMANCE WOOD FOR RESILIENT AND POTENTIALLY SUSTAINABLE FOUNDATION SYSTEMS
No full textRecent research into sustainable construction material alternatives has led to the development of High-Performance Wood (HPW), an innovative material with improved mechanical performance. HPW is produced through a two-step process, including partial delignification followed by hot-pressing densification. This dissertation explores the potential of HPW for sustainable and resilient foundation systems. The chemical, morphological, and mechanical properties of millimeter-scale HPW samples produced under various partial delignification and densification conditions were investigated. The results showed significant lignin and hemicellulose removal, which was associated with enhanced crystallinity and mechanical properties. Moreover, reduction of lignin content below 10% has resulted in wood strength reduction. To address challenges associated with scaling up the HPW production, a pressurized partial delignification method was developed to achieve deeper and more uniform chemical penetration through the wood samples. This technique enhanced the diffusion of chemicals, accelerated the removal of lignin and hemicellulose, and reduced treatment time. However, it also led to excessive delignification near the sample edges, which caused localized reductions in mechanical properties. The potential of HPW as a deep foundation material was assessed through lab-scale lateral and axial pull-out load tests, which showed that HPW piles can improve driving efficiency, reduce axial deformation under pull-out loading, and enhance the overall lateral load resistance. A Life Cycle Assessment (LCA) was also conducted to evaluate the environmental impacts of lab-scale HPW piles. Global Warming Potential (GWP) impact category, which was driven by electricity consumption during hot-pressing and boiling. The GWP of batched produced HPW piles was comparable to and higher than steel and concrete piles with equivalent stiffness, respectively. This is due to the lab-scale nature of HPW production, which can be potentially reduced by scaling up the production process
Raw Data for New Layered Quaternary Zintl Pnictide Oxides
No full textThree new heteroanionic oxypnictides, Ba2Zn2Sb2O, Ba2Zn2Bi2O, and the solid solution Ba2Zn2Sb2−xBixO (x ≈ 1.1–1.6), have been synthesized and structurally characterized. They are isostructural with their Mn-bearing analog, adopting the Ba2Mn2Sb2O-type structure (space group P63/mmc, No. 194), and feature a double-layered 2D [Zn2Pn2O]2- substructure (Pn = Sb, Bi, Sb/Bi) composed of corner-sharing, distorted tetrahedral ZnPn3O units. Electronic structure calculations reveal a systematic progression from semiconducting Ba2Zn2Sb2O to metallic Ba2Zn2Bi2O as Bi content increases. These trends are corroborated by transport property measurements, with Ba2Zn2Sb0.9(1)Bi1.1O exhibiting relatively low electrical resistivity, high Hall mobilities of ∼ 160 cm2/V·s, and large Seebeck coefficients from 69 to 132 μV/K over the 300–600 K temperature range. Comparison with structurally related Zintl pnictides, such as SrIn2As2 and PrZn3As3 phases, situates Ba2Zn2Pn2O (Pn = Sb, Bi) within a broader family of heteroanionic oxypnictide Zintl compounds, highlighting their structural flexibility and amenability to band engineering. Electronic structure and bonding considerations point to tunable semiconducting behavior and underscore the relevance of these materials for thermoelectric and topological applications
OPTIMIZING THE IMPACTS OF TRUCK PLATOONING ON HIGHWAYS NETWORK CONSIDERING HUMAN-AUTOMATED INTERACTIONS IN A MIXED ROAD ENVIRONMENT
No full textConnected and automated truck platooning (CAT) offers significant potential for improving road transportation efficiency, sustainability, and safety. While past studies typically isolated impacts on fuel consumption, safety, or pavement performance, this research comprehensively examines truck platooning configurations, including platoon size, headway distances, lane use, and market penetration, considering interactions with human-driven vehicles.
This dissertation achieves five main objectives: (1) assessing truck platoon configurations\u27 impact on fuel consumption; (2) exploring traffic operation and safety impacts, including drivers\u27 merging/diverging behaviors; (3) analyzing lane-change strategies\u27 effects on safety and operational efficiency; (4) evaluating overall highway safety and efficiency impacts; and (5) investigating impacts on pavement across climatic zones.
Field experiments demonstrated that negative binomial regression models most accurately (74%) predict fuel savings, revealing increased platoon size and decreased spacing can yield fuel savings up to 16%. Driving simulator experiments involving 85 participants indicated increasing headway distances to 60 feet improved merging efficiency, reducing Time-to-Merge (TTM) by 44.6% to 4.1 seconds. Additionally, the First Vehicle Changes Lane First (FVCLF) strategy enhanced traffic safety and efficiency, increasing average Time-to-Collision (TTC) to 3.145 seconds and reducing delay by approximately 28.8% compared to Last Vehicle Changes Lane First (LVCLF).
Microsimulation analysis combined with Structural Equation Modeling (SEM) across 257 scenarios further confirmed FVCLF’s superior performance, reducing vehicle delay by 4.62 seconds and Time-to-Diverge (TTD) by 2.92 seconds per vehicle. Pavement analysis using mechanistic-empirical modeling found shorter truck spacing significantly increased pavement damage, particularly rutting by 18.2% and fatigue cracking by up to 376%. Damage intensified in dry-freeze climates; for example, rutting increased from 9 mm to 15 mm when increasing platoon size from two to five trucks, and AC layer rutting doubled. Increasing spacing from 6.5 to 30 feet notably reduced rutting by nearly 20%.
These findings emphasize the critical need for balanced platoon configurations, recommending specific strategies for policymakers and planners aiming to optimize benefits while minimizing negative pavement and safety impacts, thus enhancing road transportation sustainability and efficiency